WebCARMA: A web application for the functional and taxonomic classification of unassembled metagenomic reads

BMC Bioinformatics

Volumn 10, Issue , 2009, Pages

  Gerlach, Wolfgang ^a   Jünemann, Sebastian ^a,b   Tille, Felix ^a   Goesmann, Alexander ^a   Stoye, Jens ^a  

^a BIELEFELD UNIVERSITY   (Germany)

^b UNIVERSITY HOSPITAL MÜNSTER   (Germany)

Author keywords

[No Author keywords available]

Indexed keywords

FUNCTIONAL CLASSIFICATION; GENETIC POTENTIAL; HIGH-THROUGHPUT SEQUENCING; METAGENOMICS; MICROBIAL COMMUNITIES; SOFTWARE PIPELINE; SPECIES COMPOSITION; WEB APPLICATION;

APPLICATIONS;

WORLD WIDE WEB;

ARTICLE; BIOREACTOR; COMPUTER PROGRAM; CONTROLLED STUDY; FUNCTIONAL GENOMICS; GENOME SIZE; INTERNET; METAGENOMICS; MICROBIAL COMMUNITY; MICROBIAL GENETICS; SIMULATION; SPECIES COMPOSITION; TAXONOMY; BIOLOGY; GENOME; GENOMICS; METHODOLOGY;

COMPUTATIONAL BIOLOGY; GENOME; GENOMICS; INTERNET; METAGENOMICS; SOFTWARE;

EID: 74049132798     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-10-430     Document Type: Article

References (38)

1. Schloss PD, Handelsman J. Metagenomics for studying unculturable microorganisms: cutting the Gordian knot. Genome Biol 2005, 6(8):229. 10.1186/gb-2005-6-8-229, 1273625, 16086859.
2. Breitbart M, Salamon P, Andresen B, Mahaffy JM, Segall AM, Mead D, Azam F, Rohwer F. Genomic analysis of uncultured marine viral communities. Proc Natl Acad Sci USA 2002, 99(22):14250-14255. 10.1073/pnas.202488399, 137870, 12384570.
3. Tyson GW, Chapman J, Hugenholtz P, Allen EE, Ram RJ, Richardson PM, Solovyev VV, Rubin EM, Rokhsar DS, Banfield JF. Community structure and metabolism through reconstruction of microbial genomes from the environment. Nature 2004, 428(6978):37-43. 10.1038/nature02340, 14961025.
4. Venter JC, Remington K, Heidelberg JF, Halpern AL, Rusch D, Eisen JA, Wu D, Paulsen I, Nelson KE, Nelson W, Fouts DE, Levy S, Knap AH, Lomas MW, Nealson K, White O, Peterson J, Hoffman J, Parsons R, Baden-Tillson H, Pfannkoch C, Rogers YH, Smith HO. Environmental genome shotgun sequencing of the Sargasso Sea. Science 2004, 304(5667):66-74. 10.1126/science.1093857, 15001713.
5. Karlin S, Mrázek J, Campbell AM. Compositional biases of bacterial genomes and evolutionary implications. J Bacteriol 1997, 179(12):3899-3913. 179198, 9190805.
6. Campbell A, Mrázek J, Karlin S. Genome signature comparisons among prokaryote, plasmid, and mitochondrial DNA. Proc Natl Acad Sci USA 1999, 96(16):9184-9189. 10.1073/pnas.96.16.9184, 17754, 10430917.
7. McHardy AC, Martín HG, Tsirigos A, Hugenholtz P, Rigoutsos I. Accurate phylogenetic classification of variable-length DNA fragments. Nat Methods 2007, 4:63-72. 10.1038/nmeth976, 17179938.
8. Teeling H, Waldmann J, Lombardot T, Bauer M, Glöckner FO. TETRA: a web-service and a stand-alone program for the analysis and comparison of tetranucleotide usage patterns in DNA sequences. BMC Bioinformatics 2004, 5:163. 10.1186/1471-2105-5-163, 529438, 15507136.
9. Abe T, Sugawara H, Kinouchi M, Kanaya S, Ikemura T. Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples. DNA Res 2005, 12(5):281-290. 10.1093/dnares/dsi015, 16769690.
10. Diaz NN, Krause L, Goesmann A, Niehaus K, Nattkemper TW. TACOA: taxonomic classification of environmental genomic fragments using a kernelized nearest neighbor approach. BMC Bioinformatics 2009, 10:56. 10.1186/1471-2105-10-56, 2653487, 19210774.
11. Huson DH, Auch AF, Qi J, Schuster SC. MEGAN analysis of metagenomic data. Genome Res 2007, 17(3):377-386. 10.1101/gr.5969107, 1800929, 17255551.
12. Meyer F, Paarmann D, D'Souza M, Olson R, Glass EM, Kubal M, Paczian T, Rodriguez A, Stevens R, Wilke A, Wilkening J, Edwards RA. The metagenomics RAST server - a public resource for the automatic phylogenetic and functional analysis of metagenomes. BMC Bioinformatics 2008, 9:386. 10.1186/1471-2105-9-386, 2563014, 18803844.
13. Pushkarev D, Neff NF, Quake SR. Single-molecule sequencing of an individual human genome. Nature Biotechnology 2009, 27:847-850. 10.1038/nbt.1561, 19668243.
14. Wommack EK, Bhavsar J, Ravel J. Metagenomics: Read length matters. Appl Environ Microbiol 2008, 74(5):1453-1463. 10.1128/AEM.02181-07, 2258652, 18192407.
15. Krause L, Diaz NN, Goesmann A, Kelley S, Nattkemper TW, Rohwer F, Edwards RA, Stoye J. Phylogenetic classification of short environmental DNA fragments. Nucl Acids Res 2008, 36(7):2230-2239. 10.1093/nar/gkn038, 2367736, 18285365.
16. Woese CR, Fox GE. Phylogenetic structure of the prokaryotic domain: the primary kingdoms. Proc Natl Acad Sci USA 1977, 74(11):5088-5090. 10.1073/pnas.74.11.5088, 432104, 270744.
17. Woese CR. Bacterial evolution. Microbiol Rev 1987, 51(2):221-271. 373105, 2439888.
18. Giovannoni SJ, Britschgi TB, Moyer CL, Field KG. Genetic diversity in Sargasso Sea bacterioplankton. Nature 1990, 345(6270):60-63. 10.1038/345060a0, 2330053.
19. Dinsdale EA, Pantos O, Smriga S, Edwards RA, Angly F, Wegley L, Hatay M, Hall D, Brown E, Haynes M, Krause L, Sala E, Sandin SA, Thurber RV, Willis BL, Azam F, Knowlton N, Rohwer F. Microbial Ecology of Four Coral Atolls in the Northern Line Islands. PLoS ONE 2008, 3(2):e1584. 10.1371/journal.pone.0001584, 2253183, 18301735.
20. Sandin SA, Smith JE, DeMartini EE, Dinsdale EA, Donner SD, Friedlander AM, Konotchick T, Malay M, Maragos JE, Obura D, Pantos O, Paulay G, Richie M, Rohwer F, Schroeder RE, Walsh S, Jackson JBC, Knowlton N, Sala E. Baselines and Degradation of Coral Reefs in the Northern Line Islands. PLoS ONE 2008, 3(2):e1548. 10.1371/journal.pone.0001548, 2244711, 18301734.
21. Krause L, Diaz NN, Edwards RA, Gartemann KH, Krömeke H, Neuweger H, Pühler A, Runte KJ, Schlüter A, Stoye J, Szczepanowski R, Tauch A, Goesmann A. Taxonomic composition and gene content of a methane-producing microbial community isolated from a biogas reactor. J Biotechnol 2008, 136(1-2):91-101. 10.1016/j.jbiotec.2008.06.003, 18611419.
22. Simon C, Herath J, Rockstroh S, Daniel R. Rapid identification of genes encoding DNA polymerases by function-based screening of metagenomic libraries derived from glacial ice. Appl Environ Microbiol 2009, 75(9):2964-2968. 10.1128/AEM.02644-08, 2681694, 19270136.
23. Tringe SG, von Mering C, Kobayashi A, Salamov AA, Chen K, Chang HW, Podar M, Short JM, Mathur EJ, Detter JC, Bork P, Hugenholtz P, Rubin EM. Comparative metagenomics of microbial communities. Science 2005, 308(5721):554-557. 10.1126/science.1107851, 15845853.
24. Altschul SF, Gish W, Miller W, Myers EW, Lipman DJ. Basic local alignment search tool. J Mol Biol 1990, 215(3):403-410.
25. Gish W, States DJ. Identification of protein coding regions by database similarity search. Nat Genet 1993, 3(3):266-272. 10.1038/ng0393-266, 8485583.
26. Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer ELL, Bateman A. The Pfam protein families database. Nucleic Acids Res 2008, (36 Database):D281-D288. 2238907, 18039703.
27. Durbin R, Eddy S, Krogh A, Mitchison G. Biological sequence analysis 2002, Cambridge University Press.
28. Eddy SR. Profile hidden Markov models (review). Bioinformatics 1998, 14(9):755-763. 10.1093/bioinformatics/14.9.755, 9918945.
29. Saitou N, Nei M. The neighbor-joining method: a new method for reconstructing phylogenetic trees. Mol Biol Evol 1987, 4(4):406-425.
30. Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet 2000, 25:25-29. 10.1038/75556, 10802651.
31. Sayers EW, Barrett T, Benson DA, Bryant SH, Canese K, Chetvernin V, Church DM, DiCuccio M, Edgar R, Federhen S, Feolo M, Geer LY, Helmberg W, Kapustin Y, Landsman D, Lipman DJ, Madden TL, Maglott DR, Miller V, Mizrachi I, Ostell J, Pruitt KD, Schuler GD, Sequeira E, Sherry ST, Shumway M, Sirotkin K, Souvorov A, Starchenko G, Tatusova TA, Wagner L, Yaschenko E, Ye J. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 2009, (37 Database):D5-D15.
32. Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res 2009, (37 Database):D26-D31. 10.1093/nar/gkn723, 2686462, 18940867.
33. NCBI Taxonomy Statistics. , http://www.ncbi.nlm.nih.gov/Taxonomy/txstat.cgi
34. Felsenstein J. PHYLIP - Phylogeny Inference Package (Version 3.2). Cladistics 1989, 5:164-166.
35. Schlüter A, Bekel T, Diaz NN, Dondrup M, Eichenlaub R, Gartemann KH, Krahn I, Krause L, Krömeke H, Kruse O, Mussgnug JH, Neuweger H, Niehaus K, Pühler A, Runte KJ, Szczepanowski R, Tauch A, Tilker A, Viehöver P, Goesmann A. The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology. J Biotechnol 2008, 136(1-2):77-90. 10.1016/j.jbiotec.2008.05.008, 18597880.
36. Bentley DR, Balasubramanian S, Swerdlow HP, Smith GP, Milton J, Brown CG, Hall KP, Evers DJ, Barnes CL, Bignell HR, Boutell JM, Bryant J, Carter RJ, Cheetham RK, Cox AJ, Ellis DJ, Flatbush MR, Gormley NA, Humphray SJ, Irving LJ, Karbelashvili MS, Kirk SM, Li H, Liu X, Maisinger KS, Murray LJ, Obradovic B, Ost T, Parkinson ML, Pratt MR, Rasolonjatovo IMJ, Reed MT, Rigatti R, Rodighiero C, Ross MT, Sabot A, Sankar SV, Scally A, Schroth GP, Smith ME, Smith VP, Spiridou A, Torrance PE, Tzonev SS, Vermaas EH, Walter K, Wu X, Zhang L, Alam MD, Anastasi C, Aniebo IC, Bailey DMD, Bancarz IR, Banerjee S, Barbour SG, Baybayan PA, Benoit VA, Benson KF, Bevis C, Black PJ, Boodhun A, Brennan JS, Bridgham JA, Brown RC, Brown AA, Buermann DH, Bundu AA, Burrows JC, Carter NP, Castillo N, Catenazzi MCE, Chang S, Cooley RN, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fajardo KVF, Furey WS, George D, Gietzen KJ, Goddard CP, Golda GS, Granieri PA, Green DE, Gustafson DL, Hansen NF, Harnish K, Haudenschild CD, Heyer NI, Hims MM, Ho JT, Horgan AM, Hoschler K, Hurwitz S, Ivanov DV, Johnson MQ, James T, Jones TAH, Kang GD, Kerelska TH, Kersey AD, Khrebtukova I, Kindwall AP, Kingsbury Z, Kokko-Gonzales PI, Kumar A, Laurent MA, Lawley CT, Lee SE, Lee X, Liao AK, Loch JA, Lok M, Luo S, Mammen RM, Martin JW, McCauley PG, McNitt P, Mehta P, Moon KW, Mullens JW, Newington T, Ning Z, Ng BL, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Pinkard DC, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Rodriguez AC, Roe PM, Rogers J, Bacigalupo MCR, Romanov N, Romieu A, Roth RK, Rourke NJ, Ruediger ST, Rusman E, Sanches-Kuiper RM, Schenker MR, Seoane JM, Shaw RJ, Shiver MK, Short SW, Sizto NL, Sluis JP, Smith MA, Sohna JES, Spence EJ, Stevens K, Sutton N, Szajkowski L, Tregidgo CL, Turcatti G, Vandevondele S, Verhovsky Y, Virk SM, Wakelin S, Walcott GC, Wang J, Worsley GJ, Yan J, Yau L, Zuerlein M, Rogers J, Mullikin JC, Hurles ME, McCooke NJ, West JS, Oaks FL, Lundberg PL, Klenerman D, Durbin R, Smith AJ. Accurate whole human genome sequencing using reversible terminator chemistry. Nature 2008, 456(7218):53-59. 10.1038/nature07517, 2581791, 18987734.
37. Dohm JC, Lottaz C, Borodina T, Himmelbauer H. Substantial biases in ultra-short read data sets from high-throughput DNA sequencing. Nucleic Acids Res 2008, 36(16):e105. 10.1093/nar/gkn425, 2532726, 18660515.
38. Rosenkranz R, Borodina T, Lehrach H, Himmelbauer H. Characterizing the mouse ES cell transcriptome with Illumina sequencing. Genomics 2008, 92(4):187-194. 10.1016/j.ygeno.2008.05.011, 18602984.