Genome majority vote improves gene predictions

PLoS Computational Biology

Volumn 7, Issue 11, 2011, Pages

  Wall, Michael E ^a,b,c   Raghavan, Sindhu ^a,d   Cohn, Judith D ^a   Dunbar, John ^a  

^a LOS ALAMOS NATIONAL LABORATORY   (United States)

^b CENTER FOR NONLINEAR STUDIES   (United States)

^c LOS ALAMOS NATIONAL LABORATORY   (United States)

^d University of Texas at Austin   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

BIOINFORMATICS; ERRORS; ESCHERICHIA COLI; FORECASTING;

GENE MAPS; GENE PREDICTION; LOGICAL SOLUTION; MAJORITY VOTER; MICROBIAL GENOMES; ORTHOLOGOUS GENES; ORTHOLOGS; PREDICTION ERRORS; SIMPLE++;

GENES;

ACCURACY; ARTICLE; BACTERIAL GENOME; BURKHOLDERIA; CALCULATION; CONTROLLED STUDY; ESCHERICHIA COLI; GENE MAPPING; GENETIC ALGORITHM; GENETIC DATABASE; GENOME MAJORITY VOTE; INTERMETHOD COMPARISON; NONHUMAN; PREDICTION; PROBABILITY; START CODON; VALIDITY;

ESCHERICHIA COLI;

EID: 81355163885     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1002284     Document Type: Article

References (28)

1. Delcher AL, Bratke KA, Powers EC, Salzberg SL, (2007) Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 23: 673-679.
2. Besemer J, Borodovsky M, (2005) GeneMark: web software for gene finding in prokaryotes, eukaryotes and viruses. Nucleic Acids Res 33: W451-454.
3. Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, et al. (2010) Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 11: 119.
4. Dai M, Wang P, Boyd AD, Kostov G, Athey B, et al. (2005) Evolving gene/transcript definitions significantly alter the interpretation of GeneChip data. Nucleic Acids Res 33: e175.
5. Poptsova MS, Gogarten JP, (2010) Using comparative genome analysis to identify problems in annotated microbial genomes. Microbiology 156: 1909-1917.
6. Pallejà A, Harrington ED, Bork P, (2008) Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions? BMC Genomics 9: 335.
7. Dunbar J, Cohn JD, Wall ME, (2011) Consistency of gene starts among Burkholderia genomes. BMC Bioinformatics 12: 125.
8. Aziz RK, Bartels D, Best AA, DeJongh M, Disz T, et al. (2008) The RAST Server: rapid annotations using subsystems technology. BMC Genomics 9: 75.
9. Pati A, Ivanova NN, Mikhailova N, Ovchinnikova G, Hooper SD, et al. (2010) GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Methods 7: 455-457.
10. Rudd KE, (2000) EcoGene: a genome sequence database for Escherichia coli K-12. Nucleic Acids Res 28: 60-64.
11. Riley M, Abe T, Arnaud MB, Berlyn MK, Blattner FR, et al. (2006) Escherichia coli K-12: a cooperatively developed annotation snapshot-2005. Nucleic Acids Res 34: 1-9.
12. Vallenet D, Labarre L, Rouy Z, Barbe V, Bocs S, et al. (2006) MaGe: a microbial genome annotation system supported by synteny results. Nucleic Acids Res 34: 53-65.
13. Alexandersson M, Cawley S, Pachter L, (2003) SLAM: cross-species gene finding and alignment with a generalized pair hidden Markov model. Genome Res 13: 496-502.
14. Parra G, Agarwal P, Abril JF, Wiehe T, Fickett JW, et al. (2003) Comparative gene prediction in human and mouse. Genome Res 13: 108-117.
15. Flicek P, Keibler E, Hu P, Korf I, Brent MR, (2003) Leveraging the mouse genome for gene prediction in human: from whole-genome shotgun reads to a global synteny map. Genome Res 13: 46-54.
16. Korf I, Flicek P, Duan D, Brent MR, (2001) Integrating genomic homology into gene structure prediction. Bioinformatics 17 (Suppl 1): S140-148.
17. Tenney AE, Brown RH, Vaske C, Lodge JK, Doering TL, et al. (2004) Gene prediction and verification in a compact genome with numerous small introns. Genome Res 14: 2330-2335.
18. Guigó R, Dermitzakis ET, Agarwal P, Ponting CP, Parra G, et al. (2003) Comparison of mouse and human genomes followed by experimental verification yields an estimated 1,019 additional genes. Proc Natl Acad Sci U S A 100: 1140-1145.
19. Walker M, Pavlovic V, Kasif S, (2002) A comparative genomic method for computational identification of prokaryotic translation initiation sites. Nucleic Acids Res 30: 3181-3191.
20. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ, (1990) Basic local alignment search tool. J Mol Biol 215: 403-410.
21. Gross SS, Brent MR, (2006) Using multiple alignments to improve gene prediction. J Comput Biol 13: 379-393.
22. Gross SS, Do CB, Sirota M, Batzoglou S, (2007) CONTRAST: a discriminative, phylogeny-free approach to multiple informant de novo gene prediction. Genome Biol 8: R269.
23. Brent MR, (2008) Steady progress and recent breakthroughs in the accuracy of automated genome annotation. Nat Rev Genet 9: 62-73.
24. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
25. Bruno WJ, (1996) Modeling residue usage in aligned protein sequences via maximum likelihood. Mol Biol Evol 13: 1368-1374.
26. Bruno WJ, Socci ND, Halpern AL, (2000) Weighted neighbor joining: a likelihood-based approach to distance-based phylogeny reconstruction. Mol Biol Evol 17: 189-197.
27. Skophammer RG, Servin JA, Herbold CW, Lake JA, (2007) Evidence for a gram-positive, eubacterial root of the tree of life. Mol Biol Evol 24: 1761-1768.
28. Herlemann DP, Geissinger O, Ikeda-Ohtsubo W, Kunin V, Sun H, et al. (2009) Genomic analysis of "Elusimicrobium minutum," the first cultivated representative of the phylum "Elusimicrobia" (formerly termite group 1). Appl Environ Microbiol 75: 2841-2849.