Development of joint application strategies for two microbial gene finders
McHardy AC, Goesmann A, Pühler A, Meyer F (2004)
BIOINFORMATICS 20(10): 1622-1631.
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Einrichtung
Abstract / Bemerkung
Motivation: As a starting point in annotation of bacterial genomes, gene finding programs are used for the prediction of functional elements in the DNA sequence. Due to the faster pace and increasing number of genome projects currently underway, it is becoming especially important to have performant methods for this task. Results: This study describes the development of joint application strategies that combine the strengths of two microbial gene finders to improve the overall gene finding performance. Critica is very specific in the detection of similarity-supported genes as it uses a comparative sequence analysis-based approach. Glimmer employs a very sophisticated model of genomic sequence properties and is sensitive also in the detection of organism-specific genes. Based on a data set of 113 microbial genome sequences, we optimized a combined application approach using different parameters with relevance to the gene finding problem. This results in a significant improvement in specificity while there is similarity in sensitivity to Glimmer. The improvement is especially pronounced for GC rich genomes. The method is currently being applied for the annotation of several microbial genomes.
Erscheinungsjahr
2004
Zeitschriftentitel
BIOINFORMATICS
Band
20
Ausgabe
10
Seite(n)
1622-1631
ISSN
1367-4803
eISSN
1460-2059
Page URI
https://pub.uni-bielefeld.de/record/1607424
Zitieren
McHardy AC, Goesmann A, Pühler A, Meyer F. Development of joint application strategies for two microbial gene finders. BIOINFORMATICS. 2004;20(10):1622-1631.
McHardy, A. C., Goesmann, A., Pühler, A., & Meyer, F. (2004). Development of joint application strategies for two microbial gene finders. BIOINFORMATICS, 20(10), 1622-1631. https://doi.org/10.1093/bioinformatics/bth137
McHardy, A. C., Goesmann, Alexander, Pühler, Alfred, and Meyer, F. 2004. “Development of joint application strategies for two microbial gene finders”. BIOINFORMATICS 20 (10): 1622-1631.
McHardy, A. C., Goesmann, A., Pühler, A., and Meyer, F. (2004). Development of joint application strategies for two microbial gene finders. BIOINFORMATICS 20, 1622-1631.
McHardy, A.C., et al., 2004. Development of joint application strategies for two microbial gene finders. BIOINFORMATICS, 20(10), p 1622-1631.
A.C. McHardy, et al., “Development of joint application strategies for two microbial gene finders”, BIOINFORMATICS, vol. 20, 2004, pp. 1622-1631.
McHardy, A.C., Goesmann, A., Pühler, A., Meyer, F.: Development of joint application strategies for two microbial gene finders. BIOINFORMATICS. 20, 1622-1631 (2004).
McHardy, A. C., Goesmann, Alexander, Pühler, Alfred, and Meyer, F. “Development of joint application strategies for two microbial gene finders”. BIOINFORMATICS 20.10 (2004): 1622-1631.
Daten bereitgestellt von European Bioinformatics Institute (EBI)
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Chibana H, Oka N, Nakayama H, Aoyama T, Magee BB, Magee PT, Mikami Y., Genetics 170(4), 2005
PMID: 15937140
Complete genome sequence and analysis of the multiresistant nosocomial pathogen Corynebacterium jeikeium K411, a lipid-requiring bacterium of the human skin flora.
Tauch A, Kaiser O, Hain T, Goesmann A, Weisshaar B, Albersmeier A, Bekel T, Bischoff N, Brune I, Chakraborty T, Kalinowski J, Meyer F, Rupp O, Schneiker S, Viehoever P, Pühler A., J Bacteriol 187(13), 2005
PMID: 15968079
Tauch A, Kaiser O, Hain T, Goesmann A, Weisshaar B, Albersmeier A, Bekel T, Bischoff N, Brune I, Chakraborty T, Kalinowski J, Meyer F, Rupp O, Schneiker S, Viehoever P, Pühler A., J Bacteriol 187(13), 2005
PMID: 15968079
BRIGEP--the BRIDGE-based genome-transcriptome-proteome browser.
Goesmann A, Linke B, Bartels D, Dondrup M, Krause L, Neuweger H, Oehm S, Paczian T, Wilke A, Meyer F., Nucleic Acids Res 33(web server issue), 2005
PMID: 15980569
Goesmann A, Linke B, Bartels D, Dondrup M, Krause L, Neuweger H, Oehm S, Paczian T, Wilke A, Meyer F., Nucleic Acids Res 33(web server issue), 2005
PMID: 15980569
Living with two extremes: conclusions from the genome sequence of Natronomonas pharaonis.
Falb M, Pfeiffer F, Palm P, Rodewald K, Hickmann V, Tittor J, Oesterhelt D., Genome Res 15(10), 2005
PMID: 16169924
Falb M, Pfeiffer F, Palm P, Rodewald K, Hickmann V, Tittor J, Oesterhelt D., Genome Res 15(10), 2005
PMID: 16169924
Insights into genome plasticity and pathogenicity of the plant pathogenic bacterium Xanthomonas campestris pv. vesicatoria revealed by the complete genome sequence.
Thieme F, Koebnik R, Bekel T, Berger C, Boch J, Büttner D, Caldana C, Gaigalat L, Goesmann A, Kay S, Kirchner O, Lanz C, Linke B, McHardy AC, Meyer F, Mittenhuber G, Nies DH, Niesbach-Klösgen U, Patschkowski T, Rückert C, Rupp O, Schneiker S, Schuster SC, Vorhölter FJ, Weber E, Pühler A, Bonas U, Bartels D, Kaiser O., J Bacteriol 187(21), 2005
PMID: 16237009
Thieme F, Koebnik R, Bekel T, Berger C, Boch J, Büttner D, Caldana C, Gaigalat L, Goesmann A, Kay S, Kirchner O, Lanz C, Linke B, McHardy AC, Meyer F, Mittenhuber G, Nies DH, Niesbach-Klösgen U, Patschkowski T, Rückert C, Rupp O, Schneiker S, Schuster SC, Vorhölter FJ, Weber E, Pühler A, Bonas U, Bartels D, Kaiser O., J Bacteriol 187(21), 2005
PMID: 16237009
Metagenomics: DNA sequencing of environmental samples.
Tringe SG, Rubin EM., Nat Rev Genet 6(11), 2005
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References
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