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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