Genome majority vote improves gene predictions.

Recent studies have noted extensive inconsistencies in gene start sites among orthologous genes in related microbial genomes. Here we provide the first documented evidence that imposing gene start consistency improves the accuracy of gene start-site prediction. We applied an algorithm using a genome...

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Auteurs principaux:	Michael E Wall, Sindhu Raghavan, Judith D Cohn, John Dunbar
Format:	article
Langue:	EN
Publié:	Public Library of Science (PLoS) 2011
Sujets:	Biology (General) QH301-705.5
Accès en ligne:	https://doaj.org/article/d0ed2a5550804a92ae45ece1ed78b69f
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spelling	oai:doaj.org-article:d0ed2a5550804a92ae45ece1ed78b69f2021-11-18T05:51:46ZGenome majority vote improves gene predictions.1553-734X1553-735810.1371/journal.pcbi.1002284https://doaj.org/article/d0ed2a5550804a92ae45ece1ed78b69f2011-11-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/22131910/?tool=EBIhttps://doaj.org/toc/1553-734Xhttps://doaj.org/toc/1553-7358Recent studies have noted extensive inconsistencies in gene start sites among orthologous genes in related microbial genomes. Here we provide the first documented evidence that imposing gene start consistency improves the accuracy of gene start-site prediction. We applied an algorithm using a genome majority vote (GMV) scheme to increase the consistency of gene starts among orthologs. We used a set of validated Escherichia coli genes as a standard to quantify accuracy. Results showed that the GMV algorithm can correct hundreds of gene prediction errors in sets of five or ten genomes while introducing few errors. Using a conservative calculation, we project that GMV would resolve many inconsistencies and errors in publicly available microbial gene maps. Our simple and logical solution provides a notable advance toward accurate gene maps.Michael E WallSindhu RaghavanJudith D CohnJohn DunbarPublic Library of Science (PLoS)articleBiology (General)QH301-705.5ENPLoS Computational Biology, Vol 7, Iss 11, p e1002284 (2011)
institution	DOAJ
collection	DOAJ
language	EN
topic	Biology (General) QH301-705.5
spellingShingle	Biology (General) QH301-705.5 Michael E Wall Sindhu Raghavan Judith D Cohn John Dunbar Genome majority vote improves gene predictions.
description	Recent studies have noted extensive inconsistencies in gene start sites among orthologous genes in related microbial genomes. Here we provide the first documented evidence that imposing gene start consistency improves the accuracy of gene start-site prediction. We applied an algorithm using a genome majority vote (GMV) scheme to increase the consistency of gene starts among orthologs. We used a set of validated Escherichia coli genes as a standard to quantify accuracy. Results showed that the GMV algorithm can correct hundreds of gene prediction errors in sets of five or ten genomes while introducing few errors. Using a conservative calculation, we project that GMV would resolve many inconsistencies and errors in publicly available microbial gene maps. Our simple and logical solution provides a notable advance toward accurate gene maps.
format	article
author	Michael E Wall Sindhu Raghavan Judith D Cohn John Dunbar
author_facet	Michael E Wall Sindhu Raghavan Judith D Cohn John Dunbar
author_sort	Michael E Wall
title	Genome majority vote improves gene predictions.
title_short	Genome majority vote improves gene predictions.
title_full	Genome majority vote improves gene predictions.
title_fullStr	Genome majority vote improves gene predictions.
title_full_unstemmed	Genome majority vote improves gene predictions.
title_sort	genome majority vote improves gene predictions.
publisher	Public Library of Science (PLoS)
publishDate	2011
url	https://doaj.org/article/d0ed2a5550804a92ae45ece1ed78b69f
work_keys_str_mv	AT michaelewall genomemajorityvoteimprovesgenepredictions AT sindhuraghavan genomemajorityvoteimprovesgenepredictions AT judithdcohn genomemajorityvoteimprovesgenepredictions AT johndunbar genomemajorityvoteimprovesgenepredictions
_version_	1718424756466745344

Genome majority vote improves gene predictions.

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