All Ensembl gene predictions for all vertebrate species are based on experimental evidence:
Aligning the evidences back to the gene prediction with Exonerate. Types of alignment results:
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.
- UniprotKB/Swiss-Prot
- NCBI RefSeq proteins and mRNAs
- UniprotKB/TrEMBL
- 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.
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