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 anno...

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Detalles Bibliográficos
Autores principales: Haas, Brian J, Salzberg, Steven L, Zhu, Wei, Pertea, Mihaela, Allen, Jonathan E, Orvis, Joshua, White, Owen, Buell, C Robin, Wortman, Jennifer R
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2395244/
https://www.ncbi.nlm.nih.gov/pubmed/18190707
http://dx.doi.org/10.1186/gb-2008-9-1-r7
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author Haas, Brian J
Salzberg, Steven L
Zhu, Wei
Pertea, Mihaela
Allen, Jonathan E
Orvis, Joshua
White, Owen
Buell, C Robin
Wortman, Jennifer R
author_facet Haas, Brian J
Salzberg, Steven L
Zhu, Wei
Pertea, Mihaela
Allen, Jonathan E
Orvis, Joshua
White, Owen
Buell, C Robin
Wortman, Jennifer R
author_sort Haas, Brian J
collection PubMed
description 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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spelling pubmed-23952442008-05-29 Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments Haas, Brian J Salzberg, Steven L Zhu, Wei Pertea, Mihaela Allen, Jonathan E Orvis, Joshua White, Owen Buell, C Robin Wortman, Jennifer R Genome Biol Method 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. BioMed Central 2008-01-11 /pmc/articles/PMC2395244/ /pubmed/18190707 http://dx.doi.org/10.1186/gb-2008-9-1-r7 Text en Copyright © 2008 Haas et al.; licensee BioMed Central Ltd. https://creativecommons.org/licenses/by/2.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0 (https://creativecommons.org/licenses/by/2.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
Haas, Brian J
Salzberg, Steven L
Zhu, Wei
Pertea, Mihaela
Allen, Jonathan E
Orvis, Joshua
White, Owen
Buell, C Robin
Wortman, Jennifer R
Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
title Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
title_full Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
title_fullStr Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
title_full_unstemmed Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
title_short Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments
title_sort automated eukaryotic gene structure annotation using evidencemodeler and the program to assemble spliced alignments
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2395244/
https://www.ncbi.nlm.nih.gov/pubmed/18190707
http://dx.doi.org/10.1186/gb-2008-9-1-r7
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