ORFcor: Identifying and Accommodating ORF Prediction Inconsistencies for Phylogenetic Analysis

PLoS ONE

Volumn 8, Issue 3, 2013, Pages

  Klassen, Jonathan L ^a   Currie, Cameron R ^a  

^a UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; CONSENSUS; GENETIC ALGORITHM; NONHUMAN; OPEN READING FRAME; ORTHOLOGY; PHYLOGENOMICS; PHYLOGENY; QUALITY CONTROL PROCEDURES; SENSITIVITY AND SPECIFICITY; SEQUENCE HOMOLOGY; START CODON; STOP CODON; TAXONOMIC RANK;

ALGORITHMS; COMPUTATIONAL BIOLOGY; MODELS, GENETIC; MOLECULAR SEQUENCE ANNOTATION; OPEN READING FRAMES; PHYLOGENY; PREDICTIVE VALUE OF TESTS; SENSITIVITY AND SPECIFICITY; SOFTWARE;

EID: 84874583180     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0058387     Document Type: Article

References (38)

1. Eisen JA, (1998) Phylogenomics: improving functional predictions for uncharacterized genes by evolutionary analysis. Genome Res 8: 163-167.
2. Philippe H, Delsuc F, Brinkmann H, Lartillot N, (2005) Phylogenomics. Annu Rev Ecol Evol Syst 36: 541-562.
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. Rho M, Tang H, Ye Y, (2010) FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res 38: e191.
5. Bakke P, Carney N, DeLoache W, Gearing M, Ingvorsen K, et al. (2009) Evaluation of three automated genome annotations for Halorhabdus utahensis. PLoS One 4: e6291.
6. Kislyuk A, Lomsadze A, Lapidus AL, Borodovsky M, (2009) Frameshift detection in prokaryotic genomic sequences. Int J Bioinformatics Res Appl 5: 458-477.
7. Hoff KJ, (2009) The effect of sequencing errors on metagenomic gene prediction. BMC Genomics 10: 520.
8. Klassen JL, Currie CR, (2012) Gene fragmentation in bacterial draft genomes: extent, consequences and mitigation. BMC Genomics 13: 14.
9. Hu GQ, Guo JT, Liu YC, Zhu H, (2009) MetaTISA: metagenomic translation initiation site annotator for improving gene start prediction. Bioinformatics 25: 1843-1845.
10. Salzberg SL, Phillippy AM, Zimin A, Puiu D, Magoc T, et al. (2012) GAGE: a critical evaluation of genome assemblies and assembly algorithms. Genome Res 22: 557-567.
11. Earl D, Bradnam K, St. John J, Darling A, Lin D, et al. (2011) Assemblathon 1: a competitive assessment of de novo short read assembly methods. Genome Res 21: 2224-2241.
12. Skovgaard M, Jensen LJ, Brunak S, Ussery D, Krogh A, (2001) On the total number of genes and their length distribution in complete microbial genomes. Trends Genet 17: 425-428.
13. Yu JF, Xiao K, Jiang DK, Guo J, Wang JH, et al. (2011) An integrative method for identifying the over-annotated protein-coding genes in microbial genomes. DNA Res 18: 435-449.
14. Hu GQ, Zheng X, Zhu HQ, She ZS, (2009) Prediction of translation initiation site for microbial genomes with TriTISA. Bioinformatics 25: 123-125.
15. Nielsen P, Krogh A, (2005) Large-scale prokaryotic gene prediction and comparison to genome annotation. Bioinformatics 21: 4322-4329.
16. Hu GQ, Zheng X, Ju LN, Zhu H, She ZS, (2008) Computational evaluation of TIS annotation for prokaryotic genomes. BMC Bioinformatics 9: 160.
17. Starmer J, Stomp A, Vouk M, Bitzer D, (2006) Predicting Shine-Dalgarno sequence locations exposes genome annotation errors. PLoS Comput Biol 2: e57.
18. Dunbar J, Cohn JD, Wall ME, (2011) Consistency of gene starts among Burkholderia genomes. BMC Genomics 12: 125.
19. Vallenet D, Engelen S, Mornico D, Cruveiller S, Fleury L, et al. (2009) MicroScope: a platform for microbial genome annotation and comparative genomics. Database: bap021.
20. Kislyuk AO, Katz LS, Agrawal S, Hagen MS, Conley AB, et al. (2010) A computational genomics pipeline for prokaryotic sequencing projects. Bioinformatics 26: 1819-1826.
21. Pati A, Ivanova N, Mikhailova N, Ovchinnikova G, Hooper SD, et al. (2010) GenePRIMP: a gene prediction improvement pipeline for prokaryotic genomes. Nat Meth 7: 455-457.
22. Wall ME, Raghavan S, Cohn JD, Dunbar J, (2011) Genome majority vote improves gene predictions. PLoS Comput Biol 7: e1002284.
23. Pallejà A, Harrington ED, Bork P, (2008) Large gene overlaps in prokaryotic genomes: result of functional constraints or mispredictions? BMC Genomics 9: 335.
24. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, et al. (2009) BLAST+: architecture and applications. BMC Bioinformatics 10: 421.
25. Ciccarelli FD, Doerks T, von Mering C, Creevey CJ, Snel B, et al. (2006) Toward automatic reconstruction of a highly resolved tree of life. Science 311: 1283-1287.
26. Marchler-Bauer A, Anderson JB, Derbyshire MK, DeWeese-Scott C, Gonzales NR, et al. (2007) CDD: a conserved domain database for interactive domain family analysis. Nucleic Acids Res 35: D237-D240.
27. Edgar RC, (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res 32: 1792-1797.
28. Eddy SR, (2011) Accelerated profile HMM searches. PLoS Comput Biol 7: e1002195.
29. Moran NA, McCutcheon JP, Nakabachi A, (2008) Genomics and evolution of heritable bacterial symbionts. Annu Rev Genet 42: 165-190.
30. Kristensen DM, Wolf YI, Mushegian AR, Koonin EV, (2011) Computational methods for gene orthology inference. Brief Bioinform 12: 379-391.
31. Fang G, Bhardwaj N, Robilotto R, Gerstein MB, (2010) Getting started in gene orthology and functional analysis. PLoS Comput Biol 6: e1000703.
32. Rice P, Longden I, Bleasby A, (2000) EMBOSS: the European Molecular Biology Open Software Suite. Trends Genet 16: 276-277.
33. The Gene Ontology Consortium, (2012) The Gene Ontology: enhancements for 2011. Nucleic Acids Res 40: D559-D564.
34. Rodríguez-Ezpeleta N, Embley TM, (2012) The SAR11 group of Alpha-Proteobacteria is not related to the origin of mitochondria. PLoS One 7: e30520.
35. Viklund J, Ettema TJG, Andersson SGE, (2012) Independent genome reduction and phylogenetic reclassification of the oceanic SAR11 clade. Mol Biol Evol 29: 599-615.
36. Lemmon AR, Brown JM, Stanger-Hall K, Lemmon EM, (2009) The effect of ambiguous data on phylogenetic estimates obtained by maximum likelihood and bayesian inference. Syst Biol 58: 130-145.
37. Wiens JJ, Tiu J, (2012) Highly incomplete taxa can rescue phylogenetic analyses from the negative impacts of limited taxon sampling. PLoS One 7: e42925.
38. Wiens JJ, (2006) Missing data and the design of phylogenetic analyses. J Biomed Inform 39: 34-42.