129 Sentences With "genomic sequence" | Random Sentence Generator

On January 10, scientists from Fudan University in Shanghai posted the genomic sequence of the coronavirus.

The scientists immediately reported the genomic sequence and their findings to state and federal health officials.

Scientists from Fudan University in Shanghai posted the genomic sequence of the coronavirus on January 10.

Among its accomplishments, TIGR unveiled the first complete genomic sequence of a free-living organism, the bacterium Haemophilus influenzae, in 1995.

It took 42 days for Moderna to turn the genomic sequence of the virus into a vaccine candidate and ship it to US health officials.

The first duplicative transposition occurred about 1.2mya with a second larger genomic sequence invert occurring 880,000ya.

The complete genomic sequence was determined for MULEV and found to be phylogenetically closest in structure to Bayou virus.

Sequence curation at WormBase refers to the maintenance and annotation of the primary genomic sequence and a consensus gene set.

A complete genomic sequence is available for two of the three subspecies of Y. pestis: strain KIM (of biovar Y. p. medievalis), and strain CO92 (of biovar Y. p. orientalis, obtained from a clinical isolate in the United States). As of 2006, the genomic sequence of a strain of biovar Antiqua has been recently completed.

Then, the data collection and analysis software aligns sample sequences to a known genomic sequence to identify the ChIP-DNA fragments.

C16orf86 (Chromosome 16 Open Reading Frame 86) is a gene found on the long arm of chromosome 16 at position q22.11. It has a genomic sequence that starts at 67,667,030 base pair and ends at base pair 67,668,590. Its genomic sequence is read in the forward direction with the positive strand. C16orf86 is part of the ENKD1 region.

Brandon, M. C., D. C. Wallace, and P. Baldi. 2009. Data structures and compression algorithms for genomic sequence data. Bioinformatics 25(14): 1731–1738.

CLCNKA and CLCNKB are closely related (94% sequence identity), tightly linked (separated by 11 kb of genomic sequence) and are both expressed in mammalian kidney.

The DNA Hilbert–Peano curve is a 2D color image of a genomic sequence that can highlight all structures of interest in a sequence at once.

C7orf38 is located on chromosome 7 at q22.1. Its genomic sequence contains 5,612 bp. The predominant transcript contains two exons and is 2,507 bp in length. The translated protein contains 573 amino acids.

TMEM205 is located on the minus strand of chromosome 19 from base pair 11,453,452 to 11,456,981. In close proximity to TMEM205, CCDC159 is located slightly upstream and RAB3D slightly down stream of the genomic sequence.

A plant genome assembly represents the complete genomic sequence of a plant species, which is assembled into chromosomes and other organelles by using DNA (deoxyribonucleic acid) fragments that are obtained from different types of sequencing technology.

Exome sequencing has become increasingly popular as a tool to aid in diagnosis of genetic disease because the exome contributes only 1% of the genomic sequence but accounts for roughly 85% of mutations that contribute significantly to disease.

These sequence reads are then computer assembled into overlapping or contiguous sequences (termed "contigs") which resemble the full genomic sequence once fully assembled. Sanger methods achieve read lengths of approximately 800bp (typically 500-600bp with non- enriched DNA).

The human FOXP3 genes contain 11 coding exons. Exon-intron boundaries are identical across the coding regions of the mouse and human genes. By genomic sequence analysis, the FOXP3 gene maps to the p arm of the X chromosome (specifically, Xp11.23).

During the COVID-19 pandemic, the Spallanzani Institute was the first research centre in Europe to isolate the genomic sequence of SARS-CoV-2 and upload it to GenBank. The team was composed of Maria Rosaria Capobianchi, Francesca Colavita, and Concetta Castilletti.

TMEM260 is located on band 22.3 on the small arm of human chromosome 14. The genomic sequence begins at 56,955,072 bp and ends at 57,117,324 bp on chromosome 14. The gene's genomic size is 162,253 bp. The mRNA size for TMEM260 is 4,278 bp.

FAM76A gene locusFAM76A is located on the (+) strand of the short arm of chromosome 1 (1p35.3), with the genomic sequence starting at 27725979 and ending at 27762915. The coding region is made up of 3462 base pairs and is translated into 341 amino acids.

The Modified Vaccinia Ankara (MVA) is an attenuated vaccine of a poxvirus.G. Antoine, F. Scheiflinger, F. Dorner, F. G. Falkner: The complete genomic sequence of the modified vaccinia Ankara strain: comparison with other orthopoxviruses. In: Virology. Band 244, Nummer 2, Mai 1998, , S. 365–396, , .

C9orf43 is located on the long arm of chromosome 9 at 9q32 and is expressed on the positive strand. The genomic sequence starts at 113,410,054 bp and ends at 113,429,684 bp. The gene neighborhood of C9orf43 contains 5 other genes: HDHD3, ALAD, POLE3, RGS3, and LOC105376222.

Location and size: C12orf75 is found along the plus strand of chromosome 12 (12q23.3). The gene is 40,882 bp long with the genomic sequence beginning at 105,330,636 bp and ends at 105,371,518 bp. C12orf75 contains 6 exons and is flanked by KCCAT198 (renal clear cell carcinoma- associated transcript 198).

The multiprotein complex serves to tranduce signals that involve changes in cell shape, motility or function. The published map location has been changed based on recent genomic sequence comparisons, which indicate that the expressed gene is located on chromosome 1, and a pseudogene may be located on chromosome X.

Table showing S. oneidensis MR-1 gene annotations. As a facultative anaerobe with branching electron transport pathway, S. oneidensis is considered a model organism in microbiology. In 2002, its genomic sequence was published. It has a 4.9Mb circular chromosome that is predicted to encode 4,758 protein open reading frames.

Magee and her husband have worked on the human fungal pathogen Candida albicans, and particularly their discovery of sexual mating in this fungus that had been thought to not have a mating cycle. They also made significant contributions to elucidate the genomic sequence and single nucleotide polymorphism mapping for this fungus.

The QRICH1 gene is 64,363 base pairs long, encoding an mRNA transcript that is 3331 bp in length. QRICH1 is located on chromosome 3p21.31 and contains 11 exons. The genomic sequence begins at base pair 49,057,531 and ends at base pair 49,141,201. The gene neighborhood of QRICH1 constructed by NCBI Gene.

The TMEM69 gene, located on chromosome 1p34.1, covers 7.24 kb. It is on the plus strand in the genomic sequence from 46152886 to 46160121 and encodes a primary mRNA transcript that contains 3 exons and is 6262 bp in length. Three alternative transcripts are predicted to encode the TMEM69 gene.

While studying the genome, there are some crucial aspects that should be taken in consideration. Gene prediction is the identification of genetic elements in a genomic sequence. This study is based on a combination of approaches: de novo, homology prediction, and transcription. Tools such as EvidenceModeler are used to merge the different results.

The VBRC database stores viral bioinformatic data on three levels: # Whole genomes. This level contains information about the virus species or isolate and its entire genomic sequence. # Annotated genes. This level contains all the predicted ORFs (open reading frames) in a particular virus genome, together with their DNA and (translated) protein sequences.

The complete ~203.8 Kb chloroplast genome (database accession: NC_005353) is available online. In addition to genomic sequence data, there is a large supply of expression sequence data available as cDNA libraries and expressed sequence tags (ESTs). Seven cDNA libraries are available online. A BAC library can be purchased from the Clemson University Genomics Institute.

Velvet is an algorithm package that has been designed to deal with de novo genome assembly and short read sequencing alignments. This is achieved through the manipulation of de Bruijn graphs for genomic sequence assembly via the removal of errors and the simplification of repeated regions.Zerbino, D. R.; Birney, E. (2008). “Velvet: de novo assembly using very short reads”.

As of July 2015, the most current genomic sequence for rat is available under accession numbers AABR07000001-AABR07073554 in the international sequence databases (GenBank, DDBJ and EMBL). The most current assembly is Rnor_6.0. The assembly level is "chromosome" and the genome representation is "full", including a sequence of the Y chromosome (missing from all previous assemblies).

Moreover, they implicated that a lack of C4 activity could be attributed to the structural differences between the α-chains. Nevertheless, Carroll and Porter demonstrated that there is a 1,500-bp region that acts as an intron in the genomic sequence, which they believed to be the known C4d region, a byproduct of C4 activity. Carroll et al.

When using molecular markers to study the genetics of a particular crop, it must be remembered that markers have restrictions. It should first be assessed what the genetic variability is within the organism being studied. Analyze how identifiable particular genomic sequence, near or in candidate genes. Maps can be created to determine distances between genes and differentiation between species.

In CMRD, a mutation of this genomic sequence affects the Sar1B enzyme's ability to interact with Guanine Exchange Factors (GEFs) and GTP-Activating Proteins (GAPs). The mutation of exon 6 of the sequence can eliminate the critical chain that is responsible for recognizing guanine. This strips the GTPase of its capability to hydrolyze GTP, its hallmark trait.

The number and organization of operons has been studied most critically in E. coli. As a result, predictions can be made based on an organism's genomic sequence. One prediction method uses the intergenic distance between reading frames as a primary predictor of the number of operons in the genome. The separation merely changes the frame and guarantees that the read through is efficient.

Currently, there are three ways to detect paralogs in a known genomic sequence: simple homology (FASTA), gene family evolution (TreeFam) and orthology (eggNOG v3). Since the Human Genome Project's completion, researchers are able to annotate the human genome much more easily. Using online databases like the Genome Browser at UCSC, researchers can look for homology in the sequence of their gene of interest.

SUDV is basically uncharacterized on a molecular level. However, its genomic sequence, and with it the genomic organization and the conservation of individual open reading frames, is similar to that of the other four known ebolaviruses. It is therefore currently assumed that the knowledge obtained for EBOV can be extrapolated to SUDV and that all SUDV proteins behave analogous to those of EBOV.

TAFV is basically uncharacterized on a molecular level. However, its genomic sequence, and with it the genomic organization and the conservation of individual open reading frames, is similar to that of the other four known ebolaviruses. It is therefore currently assumed that the knowledge obtained for EBOV can be extrapolated to TAFV and that all TAFV proteins behave analogous to those of EBOV.

In the mouse, Mcoln3, is located on the distal end of chromosome 3 at cytogenetic band qH2. Human and mouse TRPML3 proteins share 91% sequence identity. All vertebrate species, for which a genomic sequence is available, harbor the MCOLN3 gene. Homologs of MCOLN3 are also present in the genome of insects (Drosophila melanogaster), nematodes (Caenorhabditis elegans), sea urchin (Strongylocentrotus purpuratus) and lower organisms including Hydra and Dictyostelium.

A low-coverage genomic sequence of the northern greater galago, was completed in 2006. As a 'primitive' primate, the sequence is particularly useful in bridging the sequences of higher primates (macaque, chimp, human) to close non-primates such as rodents. The current 2x coverage is not sufficient to create a full genome assembly, but will provide comparative data across most of the human assembly.

2012, Allen et al. 2006d, Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ. (2012) Draft Genome Sequence of the Coccolithopvirus Emiliania huxleyi Virus 202. Journal of Virology 86(4):380–2381.Nissimov JI, Worthy CA, Rooks P, Napier JA, Kimmance SA, Henn MR, Ogata H, Allen MJ. (2011) Draft Genomic Sequence of the Coccolithovirus Emiliania huxleyi Virus 203.

Common limpets are believed to be able to live for up to twenty years. Patella vulgata has been the focus of a range of scientific investigation, as far back as 1935. Its development is well described and it has been the focus of transcriptomic investigation, providing a range of genomic sequence data in this species for analysis. Their teeth are the strongest natural material known.

BDBV is basically uncharacterized on a molecular level. However, its genomic sequence, and with it the genomic organization and the conservation of individual open reading frames, is similar to that of the other four known ebolaviruses (58-61% nucleotide similarity). It is therefore currently assumed that the knowledge obtained for EBOV can be extrapolated to BDBV and that all BDBV proteins are analogs of those of EBOV.

Ray has studied the ability of HIV to undergo high levels of mutation in its genomic sequence, exploring the health consequences of this mutability."HIV's Success Might Lie in Its Mutations," United Press International, November 5, 2002. In 1999, Ray and colleagues reported on the sequence diversity of HIV in India. They cautioned that different subtypes could combine, thwarting traditional efforts to develop vaccines.

In humans, the FHAD1 gene is located on chromosome 1 (1p36.21) and the genomic sequence is on the plus strand starting from 15236559 bp and ending at 15400283 bp. There are 3 main genes around FHAD1, out of which 2 encode proteins with known functions. Two genes, EFHD2 and Chymotrypsin-C (CTRC) lie downstream of FHAD1 on the plus strand. TMEM51 lies upstream of FHAD1.

The complete genomic sequence of S. sanguinis was determined in 2007 by laboratories at Virginia Commonwealth University. The genome spans 2,388,435 bp and is larger than most of the other 21 streptococcal genomes that have been sequenced. The GC content of the S. sanguinis genome is 43.4% (higher than the GC contents of other streptococci). The genome encodes 2,274 predicted proteins, 61 tRNAs, and four rRNA operons.

In the first ("knock-out"-) reaction the gene was tagged with a selectable marker, typically by insertion of a hygtk ([+/-]) cassette providing G418 resistance. In the following "knock-in" step, the tagged genomic sequence was replaced by homologous genomic sequences with certain mutations. Cell clones could then be isolated by their resistance to ganciclovir due to loss of the HSV-tk gene, i.e. ("negative selection").

It is theorized by Ross et al. 2005 and Ohno 1967 that the X chromosome is at least partially derived from the autosomal (non-sex-related) genome of other mammals, evidenced from interspecies genomic sequence alignments. The X chromosome is notably larger and has a more active euchromatin region than its Y chromosome counterpart. Further comparison of the X and Y reveal regions of homology between the two.

This gene has been reported as one of several tumor-suppressing subtransferable fragments located in the imprinted gene domain of 11p15.5, an important tumor-suppressor gene region. Alterations in this region have been associated with the Beckwith-Wiedemann syndrome, Wilms tumor, rhabdomyosarcoma, adrenocortical carcinoma, and lung, ovarian, and breast cancer. Alignment of this gene to genomic sequence data suggests that this gene may reside on chromosome 2 rather than chromosome 11.

Collagen α-1 (XXIII) chain is a protein encoded by COL23A1 gene, which is located on chromosome 5q35 in humans, and on chromosome 11B1+2 in mice. The location of this gene was discovered by genomic sequence analysis. Collagen XXIII is a type II transmembrane protein and the fourth in the subfamily of non-fibrillar transmembranous collagens. This kind of collagens have a single pass hydrophobic transmembrane domain.

Macrotermes natalensis is a fungus-growing termite species, which belongs to the genus Macrotermes, commonly reported in South Africa. This species is associated with the Termitomyces fungal genus. M. natalensis has domesticated Termitomyces to produce food for the colony. M. natalensis has become a well- studied fungus-growing termite species, and its genomic sequence reads generate 1.3 gigabytes of data, making it the largest insect genome to date.

Fungi kill insects and feed host plants BNET.com When compared to non-mycorrhizal fine roots, ectomycorrhizae may contain very high concentrations of trace elements, including toxic metals (cadmium, silver) or chlorine. The first genomic sequence for a representative of symbiotic fungi, the ectomycorrhizal basidiomycete L. bicolor, was published in 2008. An expansion of several multigene families occurred in this fungus, suggesting that adaptation to symbiosis proceeded by gene duplication.

The Moloney, Rauscher, Abelson and Friend MLVs, named for their discoverers, are used in cancer research. Endogenous MLVs are integrated into the host's germ line and are passed from one generation to the next. Stoye and Coffin have classified them into four categories by host specificity, determined by the genomic sequence of their envelope region. The ecotropic MLVs (from Gr.eco, "Home") are capable of infecting mouse cells in culture.

Artificial intelligence is providing paradigm shift toward precision medicine. Machine learning algorithms are used for genomic sequence and to analyze and draw inferences from the vast amounts of data patients and healthcare institutions recorded in every moment. AI techniques are used in precision cardiovascular medicine to understand genotypes and phenotypes in existing diseases, improve the quality of patient care, enable cost-effectiveness, and reduce readmission and mortality rates.

A low-coverage genomic sequence of the northern greater galago, O. garnettii, is in progress. As it is a 'primitive' primate, the sequence will be particularly useful in bridging the sequences of higher primates (macaque, chimpanzee, human) to close non-primates, such as rodents. The two-time planned coverage will not be sufficient to create a full genome assembly, but will provide comparative data across most of the human assembly.

The Elapoidea are a superfamily of snakes in the clade Colubroides, traditionally comprising the families Lamprophiidae and Elapidae. Advanced genomic sequence studies, however, have found lamprophiids to be paraphyletic in respect to elapids. In describing the subfamily Cyclocorinae, Weinell et al. (2017) suggested some or all subfamilies of Lamprophiidae should be reevaluated at full family status as a way to prevent the alternative, which is classifying them as elapids.

BACs are often used to sequence the genome of organisms in genome projects, for example the Human Genome Project. A short piece of the organism's DNA is amplified as an insert in BACs, and then sequenced. Finally, the sequenced parts are rearranged in silico, resulting in the genomic sequence of the organism. BACs were replaced with faster and less laborious sequencing methods like whole genome shotgun sequencing and now more recently next-gen sequencing.

Therefore, a broad, modern working definition of a gene is any discrete locus of heritable, genomic sequence which affect an organism's traits by being expressed as a functional product or by regulation of gene expression. The term gene was introduced by Danish botanist, plant physiologist and geneticist Wilhelm Johannsen in 1909. Rewritten, enlarged and translated into German as It is inspired by the ancient Greek: γόνος, gonos, that means offspring and procreation.

A wide variety of algorithms have been developed to facilitate detection of promoters in genomic sequence, and promoter prediction is a common element of many gene prediction methods. A promoter region is located before the -35 and -10 Consensus sequences. The closer the promoter region is to the consensus sequences the more often transcription of that gene will take place. There is not a set pattern for promoter regions as there are for consensus sequences.

This picture shows how Open Reading Frames (ORFs) can be used for gene prediction. Gene prediction is the process of determining where a coding gene might be in a genomic sequence. Functional proteins must begin with a Start codon (where DNA transcription begins), and end with a Stop codon (where transcription ends). By looking at where those codons might fall in a DNA sequence, one can see where a functional protein might be located.

The SL-SHC014-MA15 version of the virus, primarily engineered to infect mice, has been shown to differ 7% (over 5,000 nucleotides) from SARS-CoV-2, the cause of a human pandemic in 2019–2020. However, more studies must be completed to source credible data considering, in 2013, a study was published with accompanying data, which reports over 99% genomic sequence identies between SHC014-CoV and 3367-CoV and four random human coronaviruses.

The application of different types of encoding schemes have been explored to encode variant bases and genomic coordinates. Fixed codes, such as the Golomb code and the Rice code, are suitable when the variant or coordinate (represented as integer) distribution is well defined. Variable codes, such as the Huffman code, provide a more general entropy encoding scheme when the underlying variant and/or coordinate distribution is not well-defined (this is typically the case in genomic sequence data).

The Whitehead Institute for Biomedical Research, Center for Genome Research, was listed first (the order was according to total genomic sequence contributed). Lander was the first author named. The WICGR has also made a leading contribution to the sequencing of the mouse genome. Aside from academic interest this is an important step in fully understanding the molecular biology of mice which are often used as model organisms in studies of everything from human diseases to embryonic development.

Because of their high mutation and recombination rate and their ability to conduct horizontal gene transfer, the evolutionary history of many retroelements may be challenging to trace (Benachenhou et al., 2013). Scientists often look to the genomes of Metavirus to compare nucleic acid sequences to the sequences of other viruses, constructing lineages and proposing common ancestors. Multiple taxa of Metavirus have genomic sequence that are homologous to other genera of Metaviridae and a suggest common ancestor and/or coevolution.

A total of 66 species of Leptospira has been identified. Based on their genomic sequence, they are divided into two clades and four subclades: P1, P2, S1, and S2. The 19 members of the P1 subclade include the 8 species that can cause severe disease in humans: L. alexanderi, L. borgpetersenii, L. interrogans, L. kirschneri, L. mayottensis, L. noguchii, L. santarosai, and L. weilii. The P2 clade comprises 21 species that may cause mild disease in humans.

This gene encodes a protein involved in endoplasmic reticulum (ER)-associated degradation. The encoded protein removes unfolded proteins, accumulated during ER stress, by retrograde transport to the cytosol from the ER. This protein also uses the ubiquitin-proteasome system for additional degradation of unfolded proteins. This gene and the mitochondrial ribosomal protein L49 gene use in their respective 3' UTRs some of the same genomic sequence. Sequence analysis identified two transcript variants that encode different isoforms.

The gene encoding human SAMHD1 was originally identified in a human dendritic cell cDNA library as an orthologue of a mouse gene IFN-γ-induced gene Mg11. The SAMHD1 gene is located on chromosome 20. SAMHD1 spans 59,532 bp of genomic sequence (chromosome 20:34,954,059–35,013,590) in 16 exons and encodes a 626 amino-acid (aa) protein with a molecular weight of 72.2 kDa. SAMHD1 expressed in both cycling and noncycling cells, but the antiviral activity of SAMHD1 is limited to noncycling cells.

The SBDS gene resides in a block of genomic sequence that is locally duplicated on the chromosome. The second copy contains a non-functional version of the SBDS gene that is 97% identical to the original gene, but has accumulated inactivating mutations over time. It is considered to be a pseudogene. In a study of 158 SDS families, 75% of disease- associated mutations appeared to be the result of gene conversion, while 89% of patients harbored at least one such mutation.

S. boulardii was characterized as a species separate from S. cerevisiae because it does not digest galactose and does not undergo sporulation. Its genomic sequence, however, defines it as a clade under S. cerevisiae, closest to those found in wine. Like S. cerevisiae, it has 16 chromosomes, a 2-micron circle plasmid, and is diploid with genes for both mating types, MATa and MATα. Notably, the MATa locus consistently contains some likely disabling mutations relative to spore-forming S. cerevisiae.

A behaviour mutation is a genetic mutation that alters genes that control the way in which an organism behaves, causing their behavioural patterns to change. A mutation is a change or error in the genomic sequence of a cell. It can occur during meiosis or replication of DNA, as well as due to ionizing or UV radiation, transposons, mutagenic chemicals, viruses and a number of other factors. Mutations usually (but not always) result in a change in an organisms fitness.

Genetic maps contain information on markers (SSR, RFLP, SNP, etc.), genes, and biparental and Genome-wide Association Study (GWAS) Quantitative Trait Loci (QTL). Soybean genetic maps are displayed using the CMap comparative genetic map viewer. Soybean genomic sequence and gene model data are displayed using the GBrowse sequence viewer. Other genome annotations in this viewer include epigenetic data such as DNA methylation and gene expression data of various soybean strains subjected to different treatments and from different soybean tissues/cultivars.

7 August 2014 FDA Moves On Tekmira's Ebola Drug While Sarepta's Sits Unused By down-regulating these three proteins, TKM-Ebola inhibits virus replication and eliminates the infection. The drug was effective in rhesus monkeys infected with Ebola. After the Ebola outbreak in West Africa in 2014, the new variant responsible for it was isolated from several Ebola virus families and the specific genomic sequence was determined. The company re-designed TKM-Ebola and renamed it as "TKM-Ebola-Guinea".

The Pseudomonas phage F116 holin is a non-characterized holin homologous to one in Neisseria gonorrheae that has been characterized. This protein is the prototype of the Pseudomonas phage F116 holin (F116 Holin) family (TC# 1.E.25), which is a member of the Holin Superfamily II. Bioinformatic analysis of the genome sequence of N. gonorrhoeae revealed the presence of nine probable prophage islands. The genomic sequence of FA1090 identified five genomic regions (NgoPhi1 - 5) that are related to dsDNA lysogenic phage.

Unlike ChIP-Seq there is no size selection required before sequencing. A single sequencing run can scan for genome-wide associations with high resolution, due to the low background achieved by performing the reaction in situ with the CUT&RUN-sequencing; methodology. ChIP-Seq, by contrast, requires ten times the sequencing depth because of the intrinsically high background associated with the method. The data is then collected and analyzed using software that aligns sample sequences to a known genomic sequence to identify the CUT&Tag; DNA fragments.

Unlike ChIP- Seq there is no size selection required before sequencing. A single sequencing run can scan for genome-wide associations with high resolution, due to the low background achieved by performing the reaction in situ with the CUT&RUN- sequencing; methodology. ChIP-Seq, by contrast, requires ten times the sequencing depth because of the intrinsically high background associated with the method. The data is then collected and analyzed using software that aligns sample sequences to a known genomic sequence to identify the CUT&RUN; DNA fragments.

The main approach to manual gene annotation is to annotate transcripts aligned to the genome and take the genomic sequences as the reference rather than the cDNAs. The finished genomic sequence is analyzed using a modified Ensembl pipeline, and BLAST results of cDNAs/ESTs and proteins, along with various ab initio predictions, can be analyzed manually in the annotation browser tool Otterlace. Thus, more alternative spliced variants can be predicted compared with cDNA annotation. Moreover, genomic annotation produces a more comprehensive analysis of pseudogenes.

Batai virus is geographically spread throughout Asia and Europe. It has been shown that batai viruses from Japan, Malaysia and India share homologies in the genomic sequence more so than when virus strains from Europe and Asia are compared to each other. Reassortment of the genome can have some serious effects. It has been observed that reassortment between the M segment and the S and L segments with another strain of Batai virus (BUNV) can cause an increase in the virulence of Batai virus.

This Position Weight Matrix method turned out to be a highly accurate algorithm to detect the real splice sites and the cryptic sites in genes. He also formulated the first exon detection method, based on the requirement for splice junctions at the ends of exons, and the requirement for an Open Reading Frame that would contain the exon. This exon detection method also turned to be highly accurate, detecting most of the exons with few false positives and false negatives. He extended this approach to define a complete split gene in a eukaryotic genomic sequence.

Another advantage of miRNA-seq is that it allows the discovery of novel miRNAs that may have eluded traditional screening and profiling methods. There are several novel miRNA discovery algorithms. Their general steps are as follows: # Obtain reads that did not align to known miRNA sequences, and map them to the genome. # RNA Folding Method ## For the miRNA sequences were an exact match is found, obtain the genomic sequence including ~100bp of flanking sequence on either side, and run the RNA through RNA folding software such as the Vienna package.

It uses the Description Language for Taxonomy (DELTA) system, a world standard for taxonomic data exchange, developed at Australia's Commonwealth Scientific and Industrial Research Organisation (CSIRO). DELTA is able to store a wide diversity of data and translate it into a language suitable for traditional reports and web publication. For example, ICTVdB does not itself contain genomic sequence information but can convert DELTA data into NEXUS format. It can also handle large data inputs and is suited to compiling long lists of virus properties, text comments, and images.

The authors reported a weak but significant tendency for co-evolving pairs of residues to be co-located in the known three-dimensional structure of the proteins. The reconstruction of ancient proteins and DNA sequences has only recently become a significant scientific endeavour. The developments of extensive genomic sequence databases in conjunction with advances in biotechnology and phylogenetic inference methods have made ancestral reconstruction cheap, fast, and scientifically practical. This concept has been applied to identify co-evolving residues in protein sequences using more advanced methods for the reconstruction of phylogenies and ancestral sequences.

This low level of methylation appears to reside in genomic sequence patterns that are very different from patterns seen in humans, or in other animal or plant species to date. Genomic methylation in D. melanogaster was found at specific short motifs (concentrated in specific 5-base sequence motifs that are CA- and CT- rich but depleted of guanine) and is independent of DNMT2 activity. Further, highly sensitive mass spectrometry approaches, have now demonstrated the presence of low (0.07%) but significant levels of adenine methylation during the earliest stages of Drosophila embryogenesis.

The second permissive structure enables the HDV ribozyme to self-cleave co-transcriptionally and this structure further includes the -54/-18 nt portion of the RNA transcript. The upstream inhibitory -24/-15 stretch from the aforementioned inhibitory conformation is now sequestered in a hairpin P(-1) located upstream of the cleavage site. The P(-1) motif, however, is only found in the genomic sequence, which may be correlated with the phenomenon that genomic HDV RNA copies are more abundant in the infected liver cells. Experimental evidence also supports this alternative structure.

The γ and δ chains can be either disulfide-linked or noncovalently attached. The genomic sequence of the TRG locus has been determined in Canis lupus familiaris, with the Carnivora order hypothesized as the putative origin of the TRG locus. Forty genes were discovered of the following three types: variable (TRGV), joining (TRGJ), and constant (TRGC). These genes are organized into eight cassettes aligned with the same transcriptional orientation. Each cassette is composed of a V-J-J-C unit, except one with a J-J-C unit on the 3’ end of the locus.

To date, the Freiburg Chair of Plant Biotechnology hosts an online database of Physcomitrella patens comprising the genomic sequence, annotated gene models and supplemental information.database cosmoss.org Due to its scientific and economic importance, the genome of Physcomitrella patens has been chosen as a "flagship plant genome" by the DOE JGI in 2010.Hudson Alpha Genome Sequencing Center on flagship plant genomes Also in 1998, Reski and coworkers generated a knockout moss by deleting an ftsZ gene and thus identified the first gene essential in the division of an organelle in any eukaryote.

A concrete bioinformatic example could be a DUF606 protein, known to exist in both paired and fused copies in bacterial genomes, where a DUF606 protein (Accession: ACL39356.1) from Arthrobacter chlorophenolicus A6, has a 5+5 TM structure and matches 2 x DUF606 HMM in Pfam, and thus appears to be duplicated. When the genomic sequence (1530600 – 1531700) of the protein from Arthrobacter is obtained, it is found that it contains a palindrome ( and ) in the middle of the domain halves, although it may be too short and have too long a spacer to be able to initiate a new TID.

Diagram illustrating the development process of avian flu vaccine by reverse genetics techniques Reverse genetics is a method in molecular genetics that is used to help understand the function(s) of a gene by analysing the phenotypic effects caused by genetically engineering specific nucleic acid sequences within the gene. The process proceeds in the opposite direction to forward genetic screens of classical genetics. While forward genetics seeks to find the genetic basis of a phenotype or trait, reverse genetics seeks to find what phenotypes are controlled by particular genetic sequences. Automated DNA sequencing generates large volumes of genomic sequence data relatively rapidly.

Two SINEs may act in concert to flank and mobilize an intervening single copy DNA sequence. This was reported for a 710 bp DNA sequence upstream of the bovine beta globin gene. The DNA arrangement forms a composite transposon whose presence has been confirmed by the complete bovine genomic sequence where the mobilized sequence may be found on bovine chromosome 15 in contig NW_001493315.1 nucleotides #1085432–1086142 and the originating sequence may be found on bovine chromosome 2 in contig NW_001501789.2 nucleotides #1096679–1097389. It is likely that similar composite transposons exist in other bovine genomic regions and other mammalian genomes.

DNA sequence data from genomic and metagenomic projects are essentially the same, but genomic sequence data offers higher coverage while metagenomic data is usually highly non-redundant. Furthermore, the increased use of second-generation sequencing technologies with short read lengths means that much of future metagenomic data will be error-prone. Taken in combination, these factors make the assembly of metagenomic sequence reads into genomes difficult and unreliable. Misassemblies are caused by the presence of repetitive DNA sequences that make assembly especially difficult because of the difference in the relative abundance of species present in the sample.

The United Kingdom National DNA Database (NDNAD; officially the UK National Criminal Intelligence DNA Database) is a national DNA Database that was set up in 1995. In 2005 it had 3.1 million profiles, by 2015 it had 5.77 million and as of 2016 it has 5.86 million. The database, which was growing in 2007 by 30,000 samples each month, is populated by samples recovered from crime scenes and taken from police suspects although data for those not charged or not found guilty are deleted. Only patterns of short tandem repeats are stored in the NDNAD – not a person's full genomic sequence.

The Infectious bronchitis virus D-RNA is an RNA element known as defective RNA or D-RNA. This element is thought to be essential for viral replication and efficient packaging of avian infectious bronchitis virus (IBV) particles. Coronavirus D-RNA like that of IBV, are produced during high multiplicity of infection and contain cis-acting sequences which are required for viral replication. While it is unclear exactly how IBV D-RNA is made, it is thought to be synthesized in a similar manner as subgenomic mRNA (sg mRNA), with most of the genomic sequence left out of the product.

In yaks, hypoxia-inducible factor 1 (HIF-1) has high expression in the brain, lung and kidney, showing that it plays an important role in the adaptation to low oxygen environment. On 1 July 2012 the complete genomic sequence and analyses of a female domestic yak was announced, providing important insights into understanding mammalian divergence and adaptation at high altitude. Distinct gene expansions related to sensory perception and energy metabolism were identified. In addition, researchers also found an enrichment of protein domains related to the extracellular environment and hypoxic stress that had undergone positive selection and rapid evolution.

Workflow for DNA nanoball sequencing DNA nanoball sequencing is a high throughput sequencing technology that is used to determine the entire genomic sequence of an organism. The method uses rolling circle replication to amplify small fragments of genomic DNA into DNA nanoballs. Fluorescent nucleotides bind to complementary nucleotides and are then polymerized to anchor sequences bound to known sequences on the DNA template. The base order is determined via the fluorescence of the bound nucleotides This DNA sequencing method allows large numbers of DNA nanoballs to be sequenced per run at lower reagent costs compared to other next generation sequencing platforms.

NF1 was cloned in 1990 and its gene product neurofibromin was identified in 1992. Neurofibromin, a GTPase-activating protein, primarily regulates the protein Ras. NF1 is located on the long arm of chromosome 17, position q11.2 NF1 spans over 350-kb of genomic DNA and contains 62 exons. 58 of these exons are constitutive and 4 exhibit alternative splicing ( 9a, 10a-2, 23a, and 28a). The genomic sequence starts 4,951-bp upstream of the transcription start site and 5,334-bp upstream of the translation initiation codon, with the length of the 5’ UTR being 484-bp long.

Modern technologies have made genome sequencing accessible, and biomedical scientists have profiled genomic variation in apparently healthy individuals and individuals diagnosed with a variety of diseases. This work has led to the discovery of thousands of disease- associated genes and genetic variants, elucidating a more robust picture of the amount and types of variations found within and between humans. Proteins are encoded in genomic DNA by exons, and these comprise only ∼1% of the human genomic sequence (aka the exome). The exome of an individual carries about 6,000–10,000 amino-acid-altering nSNVs, and many of these variants are already known to be associated with more than 1000 diseases.

In order to establish the boundaries of the introns, they used the polymerase chain reaction (PCR) to amplify a fragment made from human fetal brain cDNA using two primers located in the first and fourth exon, respectively. The resulting 270 base pair (bp) long fragment was then sequenced directly in its entirety, and intron positions precisely located by comparison with the genomic sequence. Putative initiation and stop codons for the human nestin gene were found at the same positions as in the rat gene, in regions where overall similarity was very high. Based on this assumption, the human nestin gene encodes a protein with 1618 amino acids, i.e.

ZFNs can be used to disable dominant mutations in heterozygous individuals by producing double-strand breaks (DSBs) in the DNA (see Genetic recombination) in the mutant allele, which will, in the absence of a homologous template, be repaired by non-homologous end-joining (NHEJ). NHEJ repairs DSBs by joining the two ends together and usually produces no mutations, provided that the cut is clean and uncomplicated. In some instances, however, the repair is imperfect, resulting in deletion or insertion of base-pairs, producing frame-shift and preventing the production of the harmful protein. Multiple pairs of ZFNs can also be used to completely remove entire large segments of genomic sequence.

This program uses a database of confirmed transcription factor binding sites that were annotated across the human genome. A search algorithm is applied to the data set to identify possible combinations of transcription factors, which have binding sites that are close to the promoter of the gene set of interest. The possible cis- regulatory modules are then statistically analyzed and the significant combinations are graphically represented Active cis-regulatory modules in a genomic sequence have been difficult to identify. Problems in identification arise because often scientists find themselves with a small set of known transcription factors, so it makes it harder to identify statistically significant clusters of transcription factor binding sites.

There are two main ways that the term "haplotype block" is defined: one based on whether a given genomic sequence displays higher linkage disequilibrium than a predetermined threshold, and one based on whether the sequence consists of a minimum number of single nucleotide polymorphisms (SNPs) that explain a majority of the common haplotypes in the sequence (or a lower-than-usual number of unique haplotypes). In 2001, Patil et al. proposed the following definition of the term: "Suppose we have a number of haplotypes consisting of a set of consecutive SNPs. A segment of consecutive SNPs is a block if at least α percent of haplotypes are represented more than once".

This is important in gene prediction because it can reveal where coding genes are in an entire genomic sequence. In this example, a functional protein can be discovered using ORF3 because it begins with a Start codon, has multiple amino acids, and then ends with a Stop codon, all within the same reading frame. In the genomes of prokaryotes, genes have specific and relatively well-understood promoter sequences (signals), such as the Pribnow box and transcription factor binding sites, which are easy to systematically identify. Also, the sequence coding for a protein occurs as one contiguous open reading frame (ORF), which is typically many hundred or thousands of base pairs long.

DSCR1 in human is located at the centromeric border of the DSCR and encodes an inhibitor of calcineurin/ NFAT (nuclear factor activated T cells) signalling. DSCR1 genomic sequence of total 45 kb contain 7 exons and 6 introns , different cDNA analysis yield first four exons are alternative and code for two isoforms of 197 amino acids, and one isoform code for 171 amino acids which differ in their N terminal . While the rest of the 168 residues are common. There is also alternative promoter region with about 900 bp between exon 3 and 4 suggesting that the fourth isoform might be penetrated from another promoter.

T-cell and B-cell epitope mapping algorithms can computationally predict epitopes based on the genomic sequence of pathogens, without prior knowledge of a protein's structure or function. A series of steps are used to identify epitopes: # Comparison between virulent and avirulent organisms identify candidate genes that code for epitopes that solicit T-cell responses by looking for sequences that are unique to virulent strains. Additionally, differential microarray technologies can discover pathogen-specific genes that are upregulated during host-interaction and may be relevant for analysis because they are critical to the function of the pathogen. # Immunoinformatics tools predict regions of these candidate genes that interact with T cells by scanning genome-derived protein sequences of a pathogen.

Genetics compression algorithms (not to be confused with genetic algorithms) are the latest generation of lossless algorithms that compress data (typically sequences of nucleotides) using both conventional compression algorithms and specific algorithms adapted to genetic data. In 2012, a team of scientists from Johns Hopkins University published the first genetic compression algorithm that does not rely on external genetic databases for compression. HAPZIPPER was tailored for HapMap data and achieves over 20-fold compression (95% reduction in file size), providing 2- to 4-fold better compression much faster than leading general-purpose compression utilities. Genomic sequence compression algorithms, also known as DNA sequence compressors, explore the fact that DNA sequences have characteristic properties, such as inverted repeats.

Through the ENCODE pilot project, National Human Genome Research Institute (NHGRI) assessed the abilities of different approaches to be scaled up for an effort to analyse the entire human genome and to find gaps in the ability to identify functional elements in genomic sequence. The ENCODE pilot project process involved close interactions between computational and experimental scientists to evaluate a number of methods for annotating the human genome. A set of regions representing approximately 1% (30 Mb) of the human genome was selected as the target for the pilot project and was analyzed by all ENCODE pilot project investigators. All data generated by ENCODE participants on these regions was rapidly released into public databases.

The channel catfish is one of only a handful of ostariophysan freshwater fish species whose genomes have been sequenced. The channel catfish reference genome sequence was generated alongside genomic sequence data for other scaled and unscaled fish species (other catfishes, the common pleco and southern striped Raphael; also common carp), in order to provide genomic resources and aid understanding of the evolutionary loss of scales in catfishes. Results from comparative genomics and transcriptomics analyses and experiments involving channel catfish have supported a role for secretory calcium-binding phosphoproteins (SCPP) in scale formation in teleost fishes. In addition to the whole nuclear genome resources above, full mitochondrial genome sequences have been available for channel catfish since 2003.

The study of poxviruses is of great interest due to the proteins that they encode to formulate the response of the host, this makes it possible to more deeply study the relationship of the virus-host. The genomic sequence of ECTV in mice allows us to understand the mechanisms of the disease and the interaction of cells and mediators that represent host protection. The similarity of the ECTV genome with the genome of other pox viruses, of which there are 40 genomes of various genera, species and strains of poxviruses, was determined by determining their amino acid or nucleotide sequence. A study of the influence of poxviruses on human and animal health underlines the value of the ECTV mouse model.

The lethal yellow (Ay) mutation is due to an upstream deletion at the start site of agouti transcription. This deletion causes the genomic sequence of agouti to be lost, except the promoter and the first non-encoding exon of Raly, a ubiquitously expressed gene in mammals. The coding exons of agouti are placed under the control of the Raly promoter, initiating ubiquitous expression of agouti, increasing production of pheomelanin over eumelanin and resulting in the development of a yellow phenotype.Proposed mechanism for the relationship between ectopic agouti expression and the development of yellow obese syndrome The viable yellow (Avy) mutation is due to a change in the mRNA length of agouti, as the expressed gene becomes longer than the normal gene length of agouti.

Within a long region of genomic sequence, genes are often characterised by having a higher GC-content in contrast to the background GC-content for the entire genome. Evidence of GC ratio with that of length of the coding region of a gene has shown that the length of the coding sequence is directly proportional to higher G+C content. This has been pointed to the fact that the stop codon has a bias towards A and T nucleotides, and, thus, the shorter the sequence the higher the AT bias. Comparison of more than 1,000 orthologous genes in mammals showed marked within-genome variations of the third-codon position GC content, with a range from less than 30% to more than 80%.

Sharkey studies the biochemistry and biophysics that underlie plant-atmosphere interactions especially photosynthesis and isoprene emission from plants. Significant accomplishments related to photosynthesis include the measurement of carbon dioxide concentration inside leaves, measurement of the biophysical resistance to carbon dioxide diffusion within leaves, elucidation of the biochemical feedback chain that explains how limitations in starch and sucrose synthesis reduce the efficiency of photosynthesis and demonstration that maltose is the primary metabolite exported from chloroplasts at night. Significant accomplishments related to isoprene biosynthesis and emissions from plants include the first genomic sequence of an isoprene synthase, cloning isoprene synthases from ten different plant species, analysis of the evolution of isoprene synthases and enzymes needed to make the precursor to isoprene. Heat stress was shown to be ameliorated by cyclic electron flow in photosynthesis.

As an individual's genomic sequence can reveal telling medical information about themselves, and their family members, privacy proponents believe that there should be certain protections in place to ultimately protect the privacy and identity of the user from possible discrimination by insurance companies or employers, the major concern voiced. There have been instances in which genetic discrimination has occurred, often revealing how science can be misinterpreted by non-experts. In 1970, African- Americans were denied insurance coverage or charged higher premiums because they were known carriers of sickle-cell anemia, but as carriers, they do not have any medical problems themselves, and this carrier advantage actually confers resistance against malaria. The legitimacy of these policies has been challenged by scientists who condemn this attitude of genetic determinism, that genotype wholly determines phenotype.

After he joined the faculty of the University of Washington, Samudrala's Computational Biology Research Group developed a series of algorithms and web server modules to predict protein structure, function, and interactions known as Protinfo. Samudrala's group then applied these methods to entire organismal proteomes, creating a framework known as the Bioverse for exploring the relationships among the atomic, molecular, genomic, proteomic, systems, and organismal worlds. The Bioverse framework performs sophisticated analyses and predictions based on genomic sequence data to annotate and understand the interaction of protein sequence, structure, and function, both at the single molecule as well as at the systems levels. A set of first pass predictions is available for more than 50 organismal proteomes and the framework was used to annotate the finished rice genome sequence published in 2005.

Based on the split gene theory, Senapathy developed computational algorithms to detect the donor and acceptor splice sites, exons and a complete split gene in a genomic sequence. He developed the position weight matrix (PWM) method based on the frequency of the four bases at the consensus sequences of the donor and acceptor in different organisms to identify the splice sites in a given sequence. Furthermore, he formulated the first algorithm to find the exons based on the requirement of exons to contain a donor sequence (at the 5’ end) and an acceptor sequence (at the 3’ end), and an ORF in which the exon should occur, and another algorithm to find a complete split gene. These algorithms are collectively known as the Shapiro- Senapathy algorithm (S&S;).

The advent of second-generation sequencing technologies has made it possible to obtain sequence information across the entire bacterial genome at relatively modest cost and effort, and MLST can now be assigned from whole-genome sequence information, rather than sequencing each locus separately as was the practice when MLST was first developed. Whole-genome sequencing provides richer information for differentiating bacterial strains (MLST uses approximately 0.1% of the genomic sequence to assign type while disregarding the rest of the bacterial genome). For example, whole-genome sequencing of numerous isolates has revealed the single MLST lineage ST258 of Klebsiella pneumoniae comprises two distinct genetic clades, providing additional information about the evolution and spread of these multi-drug resistant organisms, and disproving the previous hypothesis of a single clonal origin for ST258.

Dr. Senapathy's original objective in developing a method for identifying splice sites was to find complete genes in raw uncharacterized genomic sequence that could be used in the human genome project. In the landmark paper with this objective, he described the basic method for identifying the splice sites within a given sequence based on the Position Weight Matrix (PWM) of the splicing sequences in different eukaryotic organism groups for the first time. He also created the first exon detection method by defining the basic characteristics of an exon as the sequence bounded by an acceptor and a donor splice sites that had S&S; scores above a threshold, and by an ORF that was mandatory for an exon. An algorithm for finding complete genes based on the identified exons was also described by Dr. Senapathy for the first time.

The Z curve method has been criticized for over analyzing the genomic sequence and including parameters that are not significant. One study analyzed 235 genomes of bacteria and determined that the z coordinate of the Z curve accounted for 99.9% of the genetic variance and the x and y coordinates were not meaningful in studying nucleotide composition. The original authors of the Z curve method have since published a rebuttal indicating that the criticisms confuse numeral smallness with biological insignificance, because variations of purine/pyrimidine and amino/keto bases (x and y components), although less than that of GC content, contain rich information that is important and useful, such as in locating replication origins of bacterial and archaeal genomes. Similar methods of visually representing genomic sequences have since been created that are better equipped to identify a broad range of genomic structures.

Some approaches used to encode and decode are: # Huffman Encoding # Adaptive Huffman Encoding # Arithmetic coding # Arithmetic coding # Context tree weighting (CTW) method The compression algorithms listed below may use one of the above encoding approaches to compress and decompress DNA database # Compression using Redundancy of DNA sets (COMRAD) # Relative Lempel-Ziv (RLZ) # GenCompress # BioCompress # DNACompress # CTW+LZ In 2012, a team of scientists from Johns Hopkins University published the first genetic compression algorithm that does not rely on external genetic databases for compression. HAPZIPPER was tailored for HapMap data and achieves over 20-fold compression (95% reduction in file size), providing 2- to 4-fold better compression much faster than leading general-purpose compression utilities. Genomic sequence compression algorithms, also known as DNA sequence compressors, explore the fact that DNA sequences have characteristic properties, such as inverted repeats. The most successful compressors are XM and GeCo.

Most of what is known about the genus Acidithiobacillus comes from experimentation and genomic analyses of two of its species: A. ferrooxidans and A. caldus. With a length of 2,932,225 base pairs, the genomic sequence of A. caldus is GC-rich with a GC content (mol%) in the range of 63.1-63.9% for strain KU and 61.7% for strain BC13. DNA hybridization studies have revealed that strains KU and BC13 exhibited 100% homology with each other, yet showed no DNA hybridization of significance (2-20%) with other species in the genus including A. ferrooxidans and A. thiooxidans, or with other similar Proteobacteria, such as Thiomonas cuprina or Thiobacillus thioparus. Strains of A. caldus have been differentiated from other related acidithiobacilli, including A. ferrooxidans and A. thiooxidans, by sequence analyses of the PCR-amplified 16S-23S rDNA intergenic spacer (ITS) and restriction fragment length polymorphism.

Overview of signal transduction pathways According to the interpretation of Systems Biology as the ability to obtain, integrate and analyze complex data sets from multiple experimental sources using interdisciplinary tools, some typical technology platforms are phenomics, organismal variation in phenotype as it changes during its life span; genomics, organismal deoxyribonucleic acid (DNA) sequence, including intra- organismal cell specific variation. (i.e., telomere length variation); epigenomics/epigenetics, organismal and corresponding cell specific transcriptomic regulating factors not empirically coded in the genomic sequence. (i.e., DNA methylation, Histone acetylation and deacetylation, etc.); transcriptomics, organismal, tissue or whole cell gene expression measurements by DNA microarrays or serial analysis of gene expression; interferomics, organismal, tissue, or cell-level transcript correcting factors (i.e., RNA interference), proteomics, organismal, tissue, or cell level measurements of proteins and peptides via two-dimensional gel electrophoresis, mass spectrometry or multi-dimensional protein identification techniques (advanced HPLC systems coupled with mass spectrometry).

The entire genomic sequence of SNV has subsequently been determined by using RNA extracted from autopsy material as well as RNA extracted from cell culture-adapted virus. The L RNA is 6562 nucleotides (nt) in length; the M RNA is 3696 nt long; and the S RNA is 2059 to 2060 nt long. When the prototype sequence (NMH15) of SNV detected in tissues from an HPS case was compared with the sequence of the SNV isolate (NMR11; isolated in Vero E6 cells from Peromyscus maniculatus trapped in the residence of the same case), only 16 nucleotide changes were found, and none of these changes resulted in alterations in amino acid sequences of viral proteins. It had been assumed that in the process of adaptation to cell culture, selection of SNV variants which grow optimally in cell culture would occur, and selected variants would differ genetically from the parental virus.

Mutations in KIF7 have also been noted in patients that present a similar phenotype to HLS and the characteristic HYLS1 A to G transformation; homozygous deletion of the KIF7 gene causes a variant form of HLS, HLS2. KIF7 encodes a structural factor vital to cilial transport, and is also implicated in other developmental disorders, such as Joubert syndrome (JS). Additionally, mutations in HYLS1 are no longer explicitly connected to HLS in humans. Homozygous mutations removing the stop codon in exon 4 of HYLS1 result in a different genomic sequence disruption to the missense mutation of HLS, and phenotypically present as JS. The ‘molar tooth sign’ of the brain, an anomaly in which cerebellar volume is reduced but cerebellar shape is retained, resembles the molar tooth and is used to identify JS. JS presents with mutations in more than 30 genes, whilst the HYLS1 mutation is the sole cause of HLS, but is also present in the HLS2 variant form with the mutated KIF7 gene.

There have been efforts to determine the evolutionary relationships between the known plant species, but phylogenies (or phylogenetic trees) created solely using morphological data, cellular structures, single enzymes, or on only a few sequences (like rRNA) can be prone to error; morphological features are especially vulnerable when two species look physically similar though they are not closely related (as a result of convergent evolution for example) or homology, or when two species closely related look very different because, for example, they are able to change in response to their environment very well. These situations are very common in the plant kingdom. An alternative method for constructing evolutionary relationships is through changes in DNA sequence of many genes between the different species which is often more robust to problems of similar-appearing species. With the amount of genomic sequence produced by this project, many predicted evolutionary relationships could be better tested by sequence alignment to improve their certainty.

The scientific community has obtained the genomic sequence of different strains of Nannochloropsis belonging to two species: N. gaditana and N. oceanica. A genome portal based on the N. gaditana B-31 genome allows accessing much of the genomic information that concerns this micro- organism, moreover dedicated web pages are also available for the genomes of N. gaditana CCMP526 and N. oceanica CCMP1779. The genomes of the sequenced Nannochloropsis strains were between 28.5 and 29 Mega bases long, they had high density of genes, reduced intron content, short intergenic regions and very limited presence of repetitive sequences. The genes of the two species share extended similarity. The analysis of the genomes revealed that these microalgae have set of genes for the synthesis and incorporation in the cell wall of cellulose and sulfated fucans and that they are able to store carbon in polymers of β-1,3- and β-1,6-linked glucose called chrysolaminarin.

In practice, localization of the gene to a chromosome or genomic region does not necessarily enable one to isolate or amplify the relevant genomic sequence. To amplify any DNA sequence in a living organism, that sequence must be linked to an origin of replication, which is a sequence of DNA capable of directing the propagation of itself and any linked sequence. However, a number of other features are needed, and a variety of specialised cloning vectors (small piece of DNA into which a foreign DNA fragment can be inserted) exist that allow protein production, affinity tagging, single stranded RNA or DNA production and a host of other molecular biology tools. Cloning of any DNA fragment essentially involves four steps # fragmentation - breaking apart a strand of DNA # ligation - gluing together pieces of DNA in a desired sequence # transfection – inserting the newly formed pieces of DNA into cells # screening/selection – selecting out the cells that were successfully transfected with the new DNA Although these steps are invariable among cloning procedures a number of alternative routes can be selected; these are summarized as a cloning strategy.