A pipeline for the systematic identification of non-redundant full-ORF cDNAs for polymorphic and evolutionary divergent genomes: Application to the ascidian Ciona intestinalis.
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.
Affiliation: Gurdon Institute, Cambridge University, Cambridge, United Kingdom. Electronic address: email@example.com.Show MeSH
Related in: MedlinePlus
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.
Affiliation: Gurdon Institute, Cambridge University, Cambridge, United Kingdom. Electronic address: firstname.lastname@example.org.