castanyes blaves

• 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.

All Ensembl gene predictions for all vertebrate species are based on experimental evidence:

1. UniprotKB/Swiss-Prot
2. NCBI RefSeq proteins and mRNAs
3. UniprotKB/TrEMBL
4. EMBL Nucleotide Sequence Archive

Aligning the evidences back to the gene prediction with Exonerate. Types of alignment results:

• perfect
• added start
• longer region
• missing start
• non-matching start
• non-matching region
• shorter region
• ...

Exonerate has an exhaustive mode that takes a lot more time but fixes some of the mini-intron and
mini-exon issues that sometimes occur. Exonerate cdna2genome is very useful for quality checking.

Genebuild now uses head-to-head alignments of genewise and exonerate, and takes the best in each case.

Some cases are still difficult to get right with algorithmic solutions: this is were the curators are needed.