Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.
EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.
Haas
Brian J
BJ
J Craig Venter Institute, The Institute for Genomic Research, Rockville, Maryland 20850, USA. bhaas@broad.mit.edu
Salzberg
Steven L
SL
Zhu
Wei
W
Pertea
Mihaela
M
Allen
Jonathan E
JE
Orvis
Joshua
J
White
Owen
O
Buell
C Robin
CR
Wortman
Jennifer R
JR
D019295:Computational Biology / Q000379:methods*; D030541:Databases, Genetic; D056890:Eukaryota / Q000235:genetics; D040461:Gene Components; D015894:Genome, Human / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics*; D006801:Humans; D012275:Oryza; D020033:Protein Isoforms / Q000235:genetics*; D012984:Software
D020033:Protein Isoforms