castanyes blaves

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.