Thousands of missed genes found in bacterial genomes and their analysis with COMBREX.
Thousands of missed genes found in bacterial genomes and their analysis with COMBREX.
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DOI：
10.1186/1745-6150-7-37
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发表时间：
2012-10-30
期刊：
影响因子：
5.5
通讯作者：
Salzberg SL
中科院分区：
文献类型：
--
作者：
Wood DE;Lin H;Levy-Moonshine A;Swaminathan R;Chang YC;Anton BP;Osmani L;Steffen M;Kasif S;Salzberg SL
The dramatic reduction in the cost of sequencing has allowed many researchers to join in the effort of sequencing and annotating prokaryotic genomes. Annotation methods vary considerably and may fail to identify some genes. Here we draw attention to a large number of likely genes missing from annotations using common tools such as Glimmer and BLAST. By analyzing 1,474 prokaryotic genome annotations in GenBank, we identify 13,602 likely missed genes that are homologs to non-hypothetical proteins, and 11,792 likely missed genes that are homologs only to hypothetical proteins, yet have supporting evidence of their protein-coding nature from COMBREX, a newly created gene function database. We also estimate the likelihood that each potential missing gene found is a genuine protein-coding gene using COMBREX. Our analysis of the causes of missed genes suggests that larger annotation centers tend to produce annotations with fewer missed genes than smaller centers, and many of the missed genes are short genes <300 bp. Over 1,000 of the likely missed genes could be associated with phenotype information available in COMBREX. 359 of these genes, found in pathogenic organisms, may be potential targets for pharmaceutical research. The newly identified genes are available on COMBREX’s website. This article was reviewed by Daniel Haft, Arcady Mushegian, and M. Pilar Francino (nominated by David Ardell).
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影响因子：
14.9
作者：
Klimke W;Agarwala R;Badretdin A;Chetvernin S;Ciufo S;Fedorov B;Kiryutin B;O'Neill K;Resch W;Resenchuk S;Schafer S;Tolstoy I;Tatusova T
通讯作者：
Tatusova T
DOI：
10.1093/database/bas003
发表时间：
2012
期刊：
Database : the journal of biological databases and curation
影响因子：
--
作者：
Eberhardt RY;Haft DH;Punta M;Martin M;O'Donovan C;Bateman A
通讯作者：
Bateman A
影响因子：
14.9
作者：
Benson DA;Cavanaugh M;Clark K;Karsch-Mizrachi I;Ostell J;Pruitt KD;Sayers EW
通讯作者：
Sayers EW
DOI：
10.1073/pnas.0335853100
发表时间：
2003-02-04
影响因子：
11.1
作者：
Brüggemann, H;Bäumer, S;Gottschalk, G
通讯作者：
Gottschalk, G
影响因子：
56.9
作者：
FLEISCHMANN, RD;ADAMS, MD;VENTER, JC
通讯作者：
VENTER, JC