Table 2 Evidence tracks used in Medicago reannotation pipeline
From: An improved genome release (version Mt4.0) for the model legume Medicago truncatula
Type | Evidence | EVM | MAKER |
|---|---|---|---|
Prediction | AUGUSTUS | Yes | Yes |
Prediction | FGENESH | Yes | Yes |
Prediction | GENEMARK | No | Yes |
Transcript | Medicago ESTs | Yes | Yes |
Transcript | RNA-seq assembled with Rnnotator | Yes | Yes |
Transcript | RNA-seq assembled with CLC | Yes | No |
Transcript | RNA-seq assembled with CUFFLINKS | Yes | No |
Transcript | Legacy Mt3.5 loci transferred using GMAP and liftOver | Yes | Yes |
Protein | Plant uniref90 proteins | Yes | Yes |
Protein | Six plant proteomes (A. thaliana, G. max, P. trichocarpa, S. lycopersicum and O. sativa) | Yes | Yes |
Protein | GENEWISE with A. thaliana, G. max and P.trichocarpa proteins | Yes | No |