castanyes blaves

Random ramblings about some random stuff, and things; but more stuff than things -- all in a mesmerizing and kaleidoscopic soapbox-like flow of words.

5/11/2009

Anolis carolinensis: First reptile in Ensembl -- Amonida Sadissa

Very few anolis proteins and cDNAs, many more ESTs.
Used Uniprot PE Evidence ranking to generate transcript models with genewise
Different parameters for Exonerate, including exhaustive option for cDNAs, including 31000 chicken set (which wasn't very useful in the end)
Chris Ponting group provided extra models and kill list to rename some retrotransposons and pseudogenes
Manually looked at some of the EST genes in Chris' list to reincorporate them in the main db

Word of advise to all Genome Sequencing Centers out there: now that RNAseq is cheap and powerful, please allocate some of your budget for that instead of spending all in genomic sequencing. Contact Sanger people for PCR-free sample preparation protocols, which makes a huge difference in terms of avoiding duplicity.

Labels: ensembl, gene prediction, scientific talk

posted by avilella # 10:33 AM

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castanyes blaves

5/11/2009

Anolis carolinensis: First reptile in Ensembl -- Amonida Sadissa

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