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Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.

ABSTRACT: 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.

SUBMITTER: Haas BJ

PROVIDER: S-EPMC2395244 | biostudies-literature | 2008 Jan

REPOSITORIES: biostudies-literature

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Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments.

Haas Brian J BJ 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

Genome biology 20080111 1

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 anno ...[more]

PMID: 18190707

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