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

Brian J. Haas; Steven L. Salzberg; Wei Zhu; Mihaela Pertea; Jonathan E. Allen; Joshua Orvis; Owen White; C. Robin Robin; Jennifer R. Wortman

doi:10.1186/gb-2008-9-1-r7

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

Brian J. Haas
, Steven L. Salzberg
, Wei Zhu
, Mihaela Pertea
, Jonathan E. Allen
, Joshua Orvis
, Owen White
, C. Robin Robin
, Jennifer R. Wortman

Research output: Contribution to journal › Article › peer-review

793 Scopus citations

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.

Original language	English (US)
Article number	R7
Journal	Genome biology
Volume	9
Issue number	1
DOIs	https://doi.org/10.1186/gb-2008-9-1-r7
State	Published - Jan 11 2008
Externally published	Yes

ASJC Scopus subject areas

Ecology, Evolution, Behavior and Systematics
Genetics
Cell Biology

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10.1186/gb-2008-9-1-r7

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@article{22b982a6366249079a614b6472683176,

title = "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.",

author = "Haas, \{Brian J.\} and Salzberg, \{Steven L.\} and Wei Zhu and Mihaela Pertea and Allen, \{Jonathan E.\} and Joshua Orvis and Owen White and Robin, \{C. Robin\} and Wortman, \{Jennifer R.\}",

note = "Funding Information: We thank Linda Hannick, Rama Maiti, Vinita Joardar, Mathangi Thiagarajan, Qi Zhao, Hernan Lorenzi, Natalie Federova, and Shu Ouyang for participating in our experiment to assess the accuracy of manual annotation in rice in the absence of rice ESTs and FL-cDNAs. We thank Bill Majoros for edification on the intricacies of gene finding. We thank Bob Zimmerman, Alan Kwan, and Matt Campbell for critiquing the manuscript. We give many thanks to Aaron Mackey and Jason Stajich for providing help and advice on using the Glean software. Work on the rice genome annotation was supported by a National Science Foundation Plant Genome Research Program grant to CRB (DBI-0321538). SLS, JEA, and MP were supported in part by NIH grant R01-LM006845 to SLS. BJH, JRW, JO, and OW were supported by MSC contract NIH-N01-AI-30071.",

year = "2008",

month = jan,

day = "11",

doi = "10.1186/gb-2008-9-1-r7",

language = "English (US)",

volume = "9",

journal = "Genome biology",

issn = "1474-7596",

publisher = "BioMed Central",

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T1 - Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

AU - Haas, Brian J.

AU - Salzberg, Steven L.

AU - Zhu, Wei

AU - Pertea, Mihaela

AU - Allen, Jonathan E.

AU - Orvis, Joshua

AU - White, Owen

AU - Robin, C. Robin

AU - Wortman, Jennifer R.

N1 - Funding Information: We thank Linda Hannick, Rama Maiti, Vinita Joardar, Mathangi Thiagarajan, Qi Zhao, Hernan Lorenzi, Natalie Federova, and Shu Ouyang for participating in our experiment to assess the accuracy of manual annotation in rice in the absence of rice ESTs and FL-cDNAs. We thank Bill Majoros for edification on the intricacies of gene finding. We thank Bob Zimmerman, Alan Kwan, and Matt Campbell for critiquing the manuscript. We give many thanks to Aaron Mackey and Jason Stajich for providing help and advice on using the Glean software. Work on the rice genome annotation was supported by a National Science Foundation Plant Genome Research Program grant to CRB (DBI-0321538). SLS, JEA, and MP were supported in part by NIH grant R01-LM006845 to SLS. BJH, JRW, JO, and OW were supported by MSC contract NIH-N01-AI-30071.

PY - 2008/1/11

Y1 - 2008/1/11

N2 - 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.

AB - 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.

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DO - 10.1186/gb-2008-9-1-r7

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SN - 1474-7596

VL - 9

JO - Genome biology

JF - Genome biology

IS - 1

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ER -

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

Abstract

ASJC Scopus subject areas

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