Short-read reading-frame predictors are not created equal: Sequence error causes loss of signal

BMC Bioinformatics

Volumn 13, Issue 1, 2012, Pages

  Trimble, William L ^a,b   Keegan, Kevin P ^a,b   D'Souza, Mark ^a,b   Wilke, Andreas ^a,b   Wilkening, Jared ^b   Gilbert, Jack ^b   Meyer, Folker ^a,b  

^a UNIVERSITY OF CHICAGO   (United States)

^b ARGONNE NATIONAL LABORATORY   (United States)

Author keywords

Gene callers, Ab initio gene prediction; Gene prediction; Reading frames; Sequence errors; Short reads

Indexed keywords

AB INITIO; ANNOTATION SYSTEMS; ARTIFICIAL DATA; CODING REGION; COMPUTATIONAL BURDEN; CONTIGS; GENE PREDICTION; HIDDEN MARKOV; LOSS-OF-SIGNAL; MOST LIKELY; READING FRAMES; SEQUENCE ANALYSIS; SEQUENCING ERRORS; SHORT READS;

ALGORITHMS; ERRORS; FORECASTING; HIDDEN MARKOV MODELS; NUCLEIC ACIDS;

GENES;

PROKARYOTA;

ALGORITHM; ARTICLE; DNA SEQUENCE; METAGENOMICS; METHODOLOGY; MOLECULAR GENETICS; NUCLEOTIDE SEQUENCE;

ALGORITHMS; BASE SEQUENCE; METAGENOMICS; MOLECULAR SEQUENCE ANNOTATION; READING FRAMES; SEQUENCE ANALYSIS, DNA;

EID: 84864201343     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-13-183     Document Type: Article

References (49)

1. Shendure J, Ji H. Next-generation DNA sequencing. Nat Biotechnol 2008, 26(10):1135-1145. 10.1038/nbt1486, 18846087.
2. Handelsman J, Tiedje J, Alvarez-Cohen I, Ashburner M, Cann I, Delong E, Doolittle F, Fraser-Liggett C, Godzik A, Gordon J, et al. The New Science of Metagenomics: Revealing the Secrets of Our Microbial Planet 2007, Washington, DC: National Academies Press.
3. McPherson J. Next-generation gap. Nat Methods 2009, 6(11s):S2-S5. 10.1038/nmeth.f.268, 19844227.
4. Ye Y, Choi J-H, Tang H. RAPSearch: a fast protein similarity search tool for short reads. BMC Bioinformatics 2011, 12(1):159. 10.1186/1471-2105-12-159, 3113943, 21575167.
5. Angiuoli S, Matalka M, Gussman A, Galens K, Vangala M, Riley D, Arze C, White J, White O, Fricke F. CloVR: a virtual machine for automated and portable sequence analysis from the desktop using cloud computing. BMC Bioinformatics 2011, 12(1):356. 10.1186/1471-2105-12-356, 3228541, 21878105.
6. Salzberg SL, Delcher AL, Kasif S, White O. Microbial gene identification using interpolated Markov models. Nucleic Acids Res 1998, 26(2):544-548. 10.1093/nar/26.2.544, 147303, 9421513.
7. Besemer J, Borodovsky M. Heuristic approach to deriving models for gene finding. Nucleic Acids Res 1999, 27(19):3911-3920. 10.1093/nar/27.19.3911, 148655, 10481031.
8. Zhu W, Lomsadze A, Borodovsky M. Ab initio gene identification in metagenomic sequences. Nucleic Acids Res 2010, 38(12):e132-e132. 10.1093/nar/gkq275, 2896542, 20403810.
9. Noguchi H, Taniguchi T, Itoh T. MetaGeneAnnotator: detecting species-specific patterns of ribosomal binding site for precise gene prediction in anonymous prokaryotic and phage genomes. DNA Res 2008, 15(6):387-396. 10.1093/dnares/dsn027, 2608843, 18940874.
10. Hoff K, Lingner T, Meinicke P, Tech M O. Predicting genes in metagenomic sequencing reads. Nucleic Acids Res 2009, 37(Web Server issue):W101-105. 2703946, 19429689.
11. Rho M, Tang H, Ye Y. FragGeneScan: predicting genes in short and error-prone reads. Nucleic Acids Res 2010, 38(20):e191-e191. 10.1093/nar/gkq747, 2978382, 20805240.
12. Hyatt D, Chen G, LoCascio P, Land M, Larimer F, Hauser L. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics 2010, 11(1):119. 10.1186/1471-2105-11-119, 2848648, 20211023.
13. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, et al. The Metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 2008, 9(1):386-388. 10.1186/1471-2105-9-386, 2563014, 18803844.
14. Wilke A, Harrison T, Wilkening J, Field D, Glass EM, Kyrpides N, Mavrommatis K, Meyer F. The M5nr: a novel non-redundant database containing protein sequences and annotations from multiple sources and associated tools. BMC Bioinformatics 2012, 13:141. 10.1186/1471-2105-13-141, 3410781, 22720753.
15. Seshadri R, Kravitz S, Smarr L, Gilna P, Frazier M. CAMERA: a community resource for metagenomics. PLoS Biol 2007, 5(3):e75. 10.1371/journal.pbio.0050075, 1821059, 17355175.
16. Tanenbaum D, Goll J, Murphy S, Kumar P, Zafar N, Thiagarajan M, Madupu R, Davidsen T, Kagan L, Kravitz S, et al. The JCVI standard operating procedure for annotating prokaryotic metagenomic shotgun sequencing data. Stand Genomic Sci 2010, 2(2):229-237. 10.4056/sigs.651139, 3035284, 21304707.
17. Arumugam M, Harrington E, Foerstner K, Raes J, Bork P. SmashCommunity: a metagenomic annotation and analysis tool. Bioinformatics 2010, 26(23):2977-2978. 10.1093/bioinformatics/btq536, 20959381.
18. Lingner T, Aßhauer K, Schreiber F, Meinicke P. CoMet--a web server for comparative functional profiling of metagenomes. Nucleic Acids Res 2011, 39(Web Server issue):W518-W523. 3125781, 21622656.
19. Markowitz V, Ivanova N, Szeto E, Palaniappan K, Chu K, Dalevi D, Chen IM, Grechkin Y, Dubchak I, Anderson I, et al. IMG/M: a data management and analysis system for metagenomes. Nucleic Acids Res 2008, 36(suppl 1):D534-D538. 2238950, 17932063.
20. Dalevi D, Ivanova N, Mavromatis K, Hooper S, Szeto E, Hugenholtz P, Kyrpides N, Markowitz V. Annotation of metagenome short reads using proxygenes. Bioinformatics 2008, 24(16):i7-i13. 10.1093/bioinformatics/btn276, 18689842.
21. Markowitz V, Chen IM, Chu K, Szeto E, Palaniappan K, Grechkin Y, Ratner A, Jacob B, Pati A, Huntemann M, et al. IMG/M: the integrated metagenome data management and comparative analysis system. Nucleic Acids Res 2012, 40(D1):D123-D129. 10.1093/nar/gkr975, 3245048, 22086953.
22. Kent J. BLAT-the BLAST-like alignment tool. Genome Res 2002, 12(4):656-664. 187518, 11932250.
23. Delcher A, Bratke K, Powers E, Salzberg S. Identifying bacterial genes and endosymbiont DNA with Glimmer. Bioinformatics 2007, 23(6):673-679. 10.1093/bioinformatics/btm009, 2387122, 17237039.
24. Margulies M, Egholm M, Altman W, Attiya S, Bader J, Bemben L, Berka J, Braverman M, Chen Y-J, Chen Z, et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 2005, 437(7057):376-380. 1464427, 16056220.
25. Huse S, Huber J, Morrison H, Sogin M, Welch D. Accuracy and quality of massively parallel DNA pyrosequencing. Genome Biol 2007, 8(7):R143. 10.1186/gb-2007-8-7-r143, 2323236, 17659080.
26. Niu B, Fu L, Sun S, Li W. Artificial and natural duplicates in pyrosequencing reads of metagenomic data. BMC Bioinforma 2010, 11(1):187.
27. Bravo H, Irizarry R. Model-based quality assessment and base-calling for second-generation sequencing data. Biometrics 2010, 66(3):665-674. 10.1111/j.1541-0420.2009.01353.x, 2888717, 19912177.
28. Gilles A, Meglécz E, Pech N, Ferreira S, Malausa T, Martin J-F. Accuracy and quality assessment of 454 GS-FLX Titanium pyrosequencing. BMC Genomics 2011, 12(1):245. 10.1186/1471-2164-12-245, 3116506, 21592414.
29. Keegan K, Trimble W, Wilkening J, Wilke A, Harrison T, D'Souza M, Meyer F. A platform-independent method for detecting errors in metagenomic sequencing data: drisee. PLoS Comput Biol 2012, 8(6):e1002541. 10.1371/journal.pcbi.1002541, 3369934, 22685393.
30. Noguchi H, Park J, Takagi T. MetaGene: prokaryotic gene finding from environmental genome shotgun sequences. Nucleic Acids Res 2006, 34(19):5623-5630. 10.1093/nar/gkl723, 1636498, 17028096.
31. Hoff K. The effect of sequencing errors on metagenomic gene prediction. BMC Genomics 2009, 10(1):520. 10.1186/1471-2164-10-520, 2781827, 19909532.
32. Prabhu VV. Symmetry observations in long nucleotide sequences. Nucleic Acids Res 1993, 21(12):2797-2800. 10.1093/nar/21.12.2797, 309655, 8332488.
33. Forsdyke DR. Relative roles of primary sequence and (G + C)% in determining the hierarchy of frequencies of complementary trinucleotide pairs in DNAs of different species. J Mol Evol 1995, 41(5):573-581.
34. Egan J, Clarke F. Source and receiver behavior in the use of a criterion. J Acoust Soc Am 1956, 28(6):1267-1269.
35. Antonov I, Borodovsky M. Genetack: frameshift identification in protein-coding sequences by the Viterbi algorithm. J Bioinform Comput Biol 2010, 8(3):535-551. 10.1142/S0219720010004847, 20556861.
36. Allen L, Allen E, Badger J, McCrow J, Paulsen I, Elbourne L, Thiagarajan M, Rusch D, Nealson K, Williamson S, et al. Influence of nutrients and currents on the genomic composition of microbes across an upwelling mosaic. ISME J 2012,
37. Hess M, Sczyrba A, Egan R, Kim T-W, Chokhawala H, Schroth G, Luo S, Clark D, Chen F, Zhang T, et al. Metagenomic discovery of biomass-degrading genes and genomes from cow rumen. Science 2011, 331(6016):463-467. 10.1126/science.1200387, 21273488.
38. Turnbaugh P, Hamady M, Yatsunenko T, Cantarel B, Duncan A, Ley R, Sogin M, Jones W, Roe B, Affourtit J, et al. A core gut microbiome in obese and lean twins. Nature 2009, 457(7228):480-484. 10.1038/nature07540, 2677729, 19043404.
39. Yok N, Rosen G. Combining gene prediction methods to improve metagenomic gene annotation. BMC Bioinformatics 2011, 12(1):20. 10.1186/1471-2105-12-20, 3042383, 21232129.
40. Konstantinidis K, Tiedje J. Trends between gene content and genome size in prokaryotic species with larger genomes. Proc Natl Acad Sci USA 2004, 101(9):3160-3165. 10.1073/pnas.0308653100, 365760, 14973198.
41. Mavromatis K, Ivanova N, Barry K, Shapiro H, Goltsman E, McHardy A, Rigoutsos I, Salamov A, Korzeniewski F, Land M, et al. Use of simulated data sets to evaluate the fidelity of metagenomic processing methods. Nat Methods 2007, 4(6):495-500. 10.1038/nmeth1043, 17468765.
42. Chin C-S, Sorenson J, Harris J, Robins W, Charles R, Jean-Charles R, Bullard J, Webster D, Kasarskis A, Peluso P, et al. The origin of the haitian cholera outbreak strain. N Engl J Med 2010, 364(1):33-42. 3030187, 21142692.
43. Rodrigue S, Materna A, Timberlake S, Blackburn M, Malmstrom R, Alm E, Chisholm S. Unlocking short read sequencing for metagenomics. PLoS One 2010, 5(7):e11840. 10.1371/journal.pone.0011840, 2911387, 20676378.
44. Foster J, Bunge J, Gilbert J, Moore J. Measuring the microbiome: perspectives on advances in DNA-based techniques for exploring microbial life. Brief Bioinform 2012, 13(4):420-429. 10.1093/bib/bbr080, 3404397, 22308073.
45. Wommack E, Bhavsar J, Ravel J. Metagenomics: read length matters. Appl Environ Microbiol 2008, 74(5):1453-1463. 10.1128/AEM.02181-07, 2258652, 18192407.
46. Pruitt K, Tatusova T, Maglott D. NCBI Reference Sequence RefSeq: a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Res 2005, 33(suppl 1):D501-D504. 539979, 15608248.
47. Richter D, Ott F, Auch A, Schmid R, Huson D. MetaSim-a sequencing simulator for genomics and metagenomics. PLoS One 2008, 3(10):e3373. 10.1371/journal.pone.0003373, 2556396, 18841204.
48. Egan J, Schulman A, Greenberg G. Operating characteristics determined by binary decisions and by ratings. J Acoust Soc Am 1959, 31(6):768-773.
49. Hoff K, Tech M, Lingner T, Daniel R, Morgenstern B, Meinicke P. Gene prediction in metagenomic fragments: a large scale machine learning approach. BMC Bioinformatics 2008, 9(1):217. 10.1186/1471-2105-9-217, 2409338, 18442389.