GISMO - gene identification using a support vector machine for ORF classification
Krause L, McHardy AC, Nattkemper TW, Pühler A, Stoye J, Meyer F (2007)
Nucleic Acids Research 35(2): 540-549.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
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Autor*in
Krause, Lutz;
McHardy, Alice C.;
Nattkemper, Tim WilhelmUniBi 
;
Pühler, AlfredUniBi ;
Stoye, JensUniBi ;
Meyer, Folker
;
Pühler, AlfredUniBi ;
Stoye, JensUniBi ;
Meyer, FolkerEinrichtung
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Centrum für Biotechnologie > Institut für Bioinformatik
Fakultät für Biologie
Technische Fakultät > AG Biodata Mining
Centrum für Biotechnologie > Arbeitsgruppe T. Nattkemper
Centrum für Biotechnologie > Arbeitsgruppe J. Stoye
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Centrum für Biotechnologie > Institut für Bioinformatik
Fakultät für Biologie
Technische Fakultät > AG Biodata Mining
Centrum für Biotechnologie > Arbeitsgruppe T. Nattkemper
Centrum für Biotechnologie > Arbeitsgruppe J. Stoye
Centrum für Biotechnologie > Institut für Genomforschung und Systembiologie
Centrum für Biotechnologie > Arbeitsgruppe A. Pühler
Abstract / Bemerkung
We present the novel prokaryotic gene finder GISMO, which combines searches for protein family domains with composition-based classification based on a support vector machine. GISMO is highly accurate; exhibiting high sensitivity and specificity in gene identification. We found that it performs well for complete prokaryotic chromosomes, irrespective of their GC content, and also for plasmids as short as 10 kb, short genes and for genes with atypical sequence composition. Using GISMO, we found several thousand new predictions for the published genomes that are supported by extrinsic evidence, which strongly suggest that these are very likely biologically active genes. The source code for GISMO is freely available under the GPL license.
Erscheinungsjahr
2007
Zeitschriftentitel
Nucleic Acids Research
Band
35
Ausgabe
2
Seite(n)
540-549
ISSN
0305-1048
eISSN
1362-4962
Page URI
https://pub.uni-bielefeld.de/record/1783345
Zitieren
Krause L, McHardy AC, Nattkemper TW, Pühler A, Stoye J, Meyer F. GISMO - gene identification using a support vector machine for ORF classification. Nucleic Acids Research. 2007;35(2):540-549.
Krause, L., McHardy, A. C., Nattkemper, T. W., Pühler, A., Stoye, J., & Meyer, F. (2007). GISMO - gene identification using a support vector machine for ORF classification. Nucleic Acids Research, 35(2), 540-549. https://doi.org/10.1093/nar/gkl1083
Krause, Lutz, McHardy, Alice C., Nattkemper, Tim Wilhelm, Pühler, Alfred, Stoye, Jens, and Meyer, Folker. 2007. “GISMO - gene identification using a support vector machine for ORF classification”. Nucleic Acids Research 35 (2): 540-549.
Krause, L., McHardy, A. C., Nattkemper, T. W., Pühler, A., Stoye, J., and Meyer, F. (2007). GISMO - gene identification using a support vector machine for ORF classification. Nucleic Acids Research 35, 540-549.
Krause, L., et al., 2007. GISMO - gene identification using a support vector machine for ORF classification. Nucleic Acids Research, 35(2), p 540-549.
L. Krause, et al., “GISMO - gene identification using a support vector machine for ORF classification”, Nucleic Acids Research, vol. 35, 2007, pp. 540-549.
Krause, L., McHardy, A.C., Nattkemper, T.W., Pühler, A., Stoye, J., Meyer, F.: GISMO - gene identification using a support vector machine for ORF classification. Nucleic Acids Research. 35, 540-549 (2007).
Krause, Lutz, McHardy, Alice C., Nattkemper, Tim Wilhelm, Pühler, Alfred, Stoye, Jens, and Meyer, Folker. “GISMO - gene identification using a support vector machine for ORF classification”. Nucleic Acids Research 35.2 (2007): 540-549.
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Dieses Objekt ist durch das Urheberrecht und/oder verwandte Schutzrechte geschützt. [...]
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2019-09-06T08:48:51Z
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Hastie T., Tibshirani R., Friedman J.H.., 2003
GS-Finder: a program to find bacterial gene start sites with a self-training method.
Ou HY, Guo FB, Zhang CT., Int. J. Biochem. Cell Biol. 36(3), 2004
PMID: 14687930
Ou HY, Guo FB, Zhang CT., Int. J. Biochem. Cell Biol. 36(3), 2004
PMID: 14687930
Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12.
Hayashi T, Makino K, Ohnishi M, Kurokawa K, Ishii K, Yokoyama K, Han CG, Ohtsubo E, Nakayama K, Murata T, Tanaka M, Tobe T, Iida T, Takami H, Honda T, Sasakawa C, Ogasawara N, Yasunaga T, Kuhara S, Shiba T, Hattori M, Shinagawa H., DNA Res. 8(1), 2001
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Codon usage in Chlamydia trachomatis is the result of strand-specific mutational biases and a complex pattern of selective forces.
Romero H, Zavala A, Musto H., Nucleic Acids Res. 28(10), 2000
PMID: 10773076
Romero H, Zavala A, Musto H., Nucleic Acids Res. 28(10), 2000
PMID: 10773076
Genome sequences of Chlamydia trachomatis MoPn and Chlamydia pneumoniae AR39.
Read TD, Brunham RC, Shen C, Gill SR, Heidelberg JF, White O, Hickey EK, Peterson J, Utterback T, Berry K, Bass S, Linher K, Weidman J, Khouri H, Craven B, Bowman C, Dodson R, Gwinn M, Nelson W, DeBoy R, Kolonay J, McClarty G, Salzberg SL, Eisen J, Fraser CM., Nucleic Acids Res. 28(6), 2000
PMID: 10684935
Read TD, Brunham RC, Shen C, Gill SR, Heidelberg JF, White O, Hickey EK, Peterson J, Utterback T, Berry K, Bass S, Linher K, Weidman J, Khouri H, Craven B, Bowman C, Dodson R, Gwinn M, Nelson W, DeBoy R, Kolonay J, McClarty G, Salzberg SL, Eisen J, Fraser CM., Nucleic Acids Res. 28(6), 2000
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Mutational and selective pressures on codon and amino acid usage in Buchnera, endosymbiotic bacteria of aphids.
Rispe C, Delmotte F, van Ham RC, Moya A., Genome Res. 14(1), 2003
PMID: 14672975
Rispe C, Delmotte F, van Ham RC, Moya A., Genome Res. 14(1), 2003
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Genome sequence of the endocellular bacterial symbiont of aphids Buchnera sp
Shigenobu S., Watanabe H., Hattori M., Sakaki Y., Ishikawa H.., 2000
Shigenobu S., Watanabe H., Hattori M., Sakaki Y., Ishikawa H.., 2000
Missing genes in metabolic pathways: a comparative genomics approach.
Osterman A, Overbeek R., Curr Opin Chem Biol 7(2), 2003
PMID: 12714058
Osterman A, Overbeek R., Curr Opin Chem Biol 7(2), 2003
PMID: 12714058
The subsystems approach to genome annotation and its use in the project to annotate 1000 genomes.
Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V., Nucleic Acids Res. 33(17), 2005
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Overbeek R, Begley T, Butler RM, Choudhuri JV, Chuang HY, Cohoon M, de Crecy-Lagard V, Diaz N, Disz T, Edwards R, Fonstein M, Frank ED, Gerdes S, Glass EM, Goesmann A, Hanson A, Iwata-Reuyl D, Jensen R, Jamshidi N, Krause L, Kubal M, Larsen N, Linke B, McHardy AC, Meyer F, Neuweger H, Olsen G, Olson R, Osterman A, Portnoy V, Pusch GD, Rodionov DA, Ruckert C, Steiner J, Stevens R, Thiele I, Vassieva O, Ye Y, Zagnitko O, Vonstein V., Nucleic Acids Res. 33(17), 2005
PMID: 16214803
The Bioperl toolkit: Perl modules for the life sciences.
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E., Genome Res. 12(10), 2002
PMID: 12368254
Stajich JE, Block D, Boulez K, Brenner SE, Chervitz SA, Dagdigian C, Fuellen G, Gilbert JG, Korf I, Lapp H, Lehvaslaiho H, Matsalla C, Mungall CJ, Osborne BI, Pocock MR, Schattner P, Senger M, Stein LD, Stupka E, Wilkinson MD, Birney E., Genome Res. 12(10), 2002
PMID: 12368254
On the total number of genes and their length distribution in complete microbial genomes.
Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A., Trends Genet. 17(8), 2001
PMID: 11485798
Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A., Trends Genet. 17(8), 2001
PMID: 11485798
Large-scale prokaryotic gene prediction and comparison to genome annotation.
Nielsen P, Krogh A., Bioinformatics 21(24), 2005
PMID: 16249266
Nielsen P, Krogh A., Bioinformatics 21(24), 2005
PMID: 16249266
Lateral gene transfer and the nature of bacterial innovation.
Ochman H, Lawrence JG, Groisman EA., Nature 405(6784), 2000
PMID: 10830951
Ochman H, Lawrence JG, Groisman EA., Nature 405(6784), 2000
PMID: 10830951
Thiamin biosynthesis in prokaryotes.
Begley TP, Downs DM, Ealick SE, McLafferty FW, Van Loon AP, Taylor S, Campobasso N, Chiu HJ, Kinsland C, Reddick JJ, Xi J., Arch. Microbiol. 171(5), 1999
PMID: 10382260
Begley TP, Downs DM, Ealick SE, McLafferty FW, Van Loon AP, Taylor S, Campobasso N, Chiu HJ, Kinsland C, Reddick JJ, Xi J., Arch. Microbiol. 171(5), 1999
PMID: 10382260
Comparative genomics of thiamin biosynthesis in procaryotes. New genes and regulatory mechanisms.
Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS., J. Biol. Chem. 277(50), 2002
PMID: 12376536
Rodionov DA, Vitreschak AG, Mironov AA, Gelfand MS., J. Biol. Chem. 277(50), 2002
PMID: 12376536
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