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AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome

BACKGROUND: A large number of gene prediction programs for the human genome exist. These annotation tools use a variety of methods and data sources. In the recent ENCODE genome annotation assessment project (EGASP), some of the most commonly used and recently developed gene-prediction programs were...

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Autores principales: Stanke, Mario, Tzvetkova, Ana, Morgenstern, Burkhard
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2006
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1810548/
https://www.ncbi.nlm.nih.gov/pubmed/16925833
http://dx.doi.org/10.1186/gb-2006-7-s1-s11
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author Stanke, Mario
Tzvetkova, Ana
Morgenstern, Burkhard
author_facet Stanke, Mario
Tzvetkova, Ana
Morgenstern, Burkhard
author_sort Stanke, Mario
collection PubMed
description BACKGROUND: A large number of gene prediction programs for the human genome exist. These annotation tools use a variety of methods and data sources. In the recent ENCODE genome annotation assessment project (EGASP), some of the most commonly used and recently developed gene-prediction programs were systematically evaluated and compared on test data from the human genome. AUGUSTUS was among the tools that were tested in this project. RESULTS: AUGUSTUS can be used as an ab initio program, that is, as a program that uses only one single genomic sequence as input information. In addition, it is able to combine information from the genomic sequence under study with external hints from various sources of information. For EGASP, we used genomic sequence alignments as well as alignments to expressed sequence tags (ESTs) and protein sequences as additional sources of information. Within the category of ab initio programs AUGUSTUS predicted significantly more genes correctly than any other ab initio program. At the same time it predicted the smallest number of false positive genes and the smallest number of false positive exons among all ab initio programs. The accuracy of AUGUSTUS could be further improved when additional extrinsic data, such as alignments to EST, protein and/or genomic sequences, was taken into account. CONCLUSION: AUGUSTUS turned out to be the most accurate ab initio gene finder among the tested tools. Moreover it is very flexible because it can take information from several sources simultaneously into consideration.
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spelling pubmed-18105482007-03-07 AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome Stanke, Mario Tzvetkova, Ana Morgenstern, Burkhard Genome Biol Research BACKGROUND: A large number of gene prediction programs for the human genome exist. These annotation tools use a variety of methods and data sources. In the recent ENCODE genome annotation assessment project (EGASP), some of the most commonly used and recently developed gene-prediction programs were systematically evaluated and compared on test data from the human genome. AUGUSTUS was among the tools that were tested in this project. RESULTS: AUGUSTUS can be used as an ab initio program, that is, as a program that uses only one single genomic sequence as input information. In addition, it is able to combine information from the genomic sequence under study with external hints from various sources of information. For EGASP, we used genomic sequence alignments as well as alignments to expressed sequence tags (ESTs) and protein sequences as additional sources of information. Within the category of ab initio programs AUGUSTUS predicted significantly more genes correctly than any other ab initio program. At the same time it predicted the smallest number of false positive genes and the smallest number of false positive exons among all ab initio programs. The accuracy of AUGUSTUS could be further improved when additional extrinsic data, such as alignments to EST, protein and/or genomic sequences, was taken into account. CONCLUSION: AUGUSTUS turned out to be the most accurate ab initio gene finder among the tested tools. Moreover it is very flexible because it can take information from several sources simultaneously into consideration. BioMed Central 2006 2006-08-07 /pmc/articles/PMC1810548/ /pubmed/16925833 http://dx.doi.org/10.1186/gb-2006-7-s1-s11 Text en Copyright © 2006 Stanke et al.; licensee BioMed Central Ltd. http://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) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research
Stanke, Mario
Tzvetkova, Ana
Morgenstern, Burkhard
AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome
title AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome
title_full AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome
title_fullStr AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome
title_full_unstemmed AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome
title_short AUGUSTUS at EGASP: using EST, protein and genomic alignments for improved gene prediction in the human genome
title_sort augustus at egasp: using est, protein and genomic alignments for improved gene prediction in the human genome
topic Research
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1810548/
https://www.ncbi.nlm.nih.gov/pubmed/16925833
http://dx.doi.org/10.1186/gb-2006-7-s1-s11
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