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A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis.

Gilchrist MJ, Sobral D, Khoueiry P, Daian F, Laporte B, Patrushev I, Matsumoto J, Dewar K, Hastings KE, Satou Y, Lemaire P, Rothbächer U - Dev. Biol. (2015)

Bottom Line: Marine organism genomes are, however, frequently highly polymorphic and encode proteins that diverge significantly from those of well-annotated model genomes.It is robust to polymorphism, includes paralog calling and does not require evolutionary proximity to well annotated model organisms.It contains 19,163 full-ORF cDNA clones covering 60% of Ciona coding genes, and full-ORF orthologs for approximately half of curated human disease-associated genes.

View Article: PubMed Central - PubMed

Affiliation: Gurdon Institute, Cambridge University, Cambridge, United Kingdom. Electronic address: mike.gilchrist@crick.ac.uk.

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Workflow of full-ORF pipeline showing novelties. Boxes show schematic workflow of the geneDistiller pipeline for the analysis and definition of full-ORF clones from a large collection. Colour blocks show major sections of process. Ovals indicate important additions or updates added in this work, the two most important conceptual novelties (vi, xi) are described in the text. The other improvements are detailed in Section 2.
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f0010: Workflow of full-ORF pipeline showing novelties. Boxes show schematic workflow of the geneDistiller pipeline for the analysis and definition of full-ORF clones from a large collection. Colour blocks show major sections of process. Ovals indicate important additions or updates added in this work, the two most important conceptual novelties (vi, xi) are described in the text. The other improvements are detailed in Section 2.

Mentions: To identify putative exons, the full-ORF clone EST sequences were aligned to the KH assembly using the EST2genome model of the Exonerate alignment programme. We ran the search at low stringency to allow for the high level of sequence divergence between type A and type B strains, using the following parameter list: –model est2genome –gapopen-15 –bestn 1 –quality 85 –percent 33 –geneseed 200 –subopt false –hspfilter 100 –maxintron 10000.


A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis.

Gilchrist MJ, Sobral D, Khoueiry P, Daian F, Laporte B, Patrushev I, Matsumoto J, Dewar K, Hastings KE, Satou Y, Lemaire P, Rothbächer U - Dev. Biol. (2015)

Workflow of full-ORF pipeline showing novelties. Boxes show schematic workflow of the geneDistiller pipeline for the analysis and definition of full-ORF clones from a large collection. Colour blocks show major sections of process. Ovals indicate important additions or updates added in this work, the two most important conceptual novelties (vi, xi) are described in the text. The other improvements are detailed in Section 2.
© Copyright Policy - CC BY
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4528069&req=5

f0010: Workflow of full-ORF pipeline showing novelties. Boxes show schematic workflow of the geneDistiller pipeline for the analysis and definition of full-ORF clones from a large collection. Colour blocks show major sections of process. Ovals indicate important additions or updates added in this work, the two most important conceptual novelties (vi, xi) are described in the text. The other improvements are detailed in Section 2.
Mentions: To identify putative exons, the full-ORF clone EST sequences were aligned to the KH assembly using the EST2genome model of the Exonerate alignment programme. We ran the search at low stringency to allow for the high level of sequence divergence between type A and type B strains, using the following parameter list: –model est2genome –gapopen-15 –bestn 1 –quality 85 –percent 33 –geneseed 200 –subopt false –hspfilter 100 –maxintron 10000.

Bottom Line: Marine organism genomes are, however, frequently highly polymorphic and encode proteins that diverge significantly from those of well-annotated model genomes.It is robust to polymorphism, includes paralog calling and does not require evolutionary proximity to well annotated model organisms.It contains 19,163 full-ORF cDNA clones covering 60% of Ciona coding genes, and full-ORF orthologs for approximately half of curated human disease-associated genes.

View Article: PubMed Central - PubMed

Affiliation: Gurdon Institute, Cambridge University, Cambridge, United Kingdom. Electronic address: mike.gilchrist@crick.ac.uk.

Show MeSH
Related in: MedlinePlus