WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads
Gerlach W, Jünemann S, Tille F, Goesmann A, Stoye J (2009)
BMC Bioinformatics 10(1): 430.
Zeitschriftenaufsatz
| Veröffentlicht | Englisch
Download
Autor*in
Einrichtung
Technische Fakultät > Computational Genomics
Centrum für Biotechnologie > Arbeitsgruppe J. Stoye
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Technische Fakultät > AG Genominformatik
Centrum für Biotechnologie > Arbeitsgruppe J. Stoye
Centrum für Biotechnologie > Institut für Bioinformatik
Centrum für Biotechnologie > Technologieplattformen > Bioinformatics Resource Facility
Centrum für Biotechnologie > Arbeitsgruppe A. Goesmann
Technische Fakultät > AG Genominformatik
Abstract / Bemerkung
Background Metagenomics is a new field of research on natural microbial communities. High-throughput sequencing techniques like 454 or Solexa-Illumina promise new possibilities as they are able to produce huge amounts of data in much shorter time and with less efforts and costs than the traditional Sanger technique. But the data produced comes in even shorter reads (35-100 basepairs with Illumina, 100-500 basepairs with 454-sequencing). CARMA is a new software pipeline for the characterisation of species composition and the genetic potential of microbial samples using short, unassembled reads. Results In this paper, we introduce WebCARMA, a refined version of CARMA available as a web application for the taxonomic and functional classification of unassembled (ultra-)short reads from metagenomic communities. In addition, we have analysed the applicability of ultra-short reads in metagenomics. Conclusions We show that unassembled reads as short as 35 bp can be used for the taxonomic classification of a metagenome. The web application is freely available at http://webcarma.cebitec.uni-bielefeld.de
Erscheinungsjahr
2009
Zeitschriftentitel
BMC Bioinformatics
Band
10
Ausgabe
1
Seite(n)
430
ISSN
1471-2105
Page URI
https://pub.uni-bielefeld.de/record/1589098
Zitieren
Gerlach W, Jünemann S, Tille F, Goesmann A, Stoye J. WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics. 2009;10(1):430.
Gerlach, W., Jünemann, S., Tille, F., Goesmann, A., & Stoye, J. (2009). WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics, 10(1), 430. https://doi.org/10.1186/1471-2105-10-430
Gerlach, Wolfgang, Jünemann, Sebastian, Tille, Felix, Goesmann, Alexander, and Stoye, Jens. 2009. “WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads”. BMC Bioinformatics 10 (1): 430.
Gerlach, W., Jünemann, S., Tille, F., Goesmann, A., and Stoye, J. (2009). WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics 10, 430.
Gerlach, W., et al., 2009. WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics, 10(1), p 430.
W. Gerlach, et al., “WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads”, BMC Bioinformatics, vol. 10, 2009, pp. 430.
Gerlach, W., Jünemann, S., Tille, F., Goesmann, A., Stoye, J.: WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads. BMC Bioinformatics. 10, 430 (2009).
Gerlach, Wolfgang, Jünemann, Sebastian, Tille, Felix, Goesmann, Alexander, and Stoye, Jens. “WebCARMA: a web application for the functional and taxonomic classification of unassembled metagenomic reads”. BMC Bioinformatics 10.1 (2009): 430.
Alle Dateien verfügbar unter der/den folgenden Lizenz(en):
Copyright Statement:
Dieses Objekt ist durch das Urheberrecht und/oder verwandte Schutzrechte geschützt. [...]
Volltext(e)
Name
Access Level
Open Access
Zuletzt Hochgeladen
2019-09-06T08:48:01Z
MD5 Prüfsumme
77a7c8c500e7f32f42a0d2be19865537
Daten bereitgestellt von European Bioinformatics Institute (EBI)
36 Zitationen in Europe PMC
Daten bereitgestellt von Europe PubMed Central.
Taxonomic and functional assignment of cloned sequences from high Andean forest soil metagenome.
Montaña JS, Jiménez DJ, Hernández M, Angel T, Baena S., Antonie Van Leeuwenhoek 101(2), 2012
PMID: 21792685
Montaña JS, Jiménez DJ, Hernández M, Angel T, Baena S., Antonie Van Leeuwenhoek 101(2), 2012
PMID: 21792685
Phylogenetic and gene-centric metagenomics of the canine intestinal microbiome reveals similarities with humans and mice.
Swanson KS, Dowd SE, Suchodolski JS, Middelbos IS, Vester BM, Barry KA, Nelson KE, Torralba M, Henrissat B, Coutinho PM, Cann IK, White BA, Fahey GC., ISME J 5(4), 2011
PMID: 20962874
Swanson KS, Dowd SE, Suchodolski JS, Middelbos IS, Vester BM, Barry KA, Nelson KE, Torralba M, Henrissat B, Coutinho PM, Cann IK, White BA, Fahey GC., ISME J 5(4), 2011
PMID: 20962874
UMARS: Un-MAppable Reads Solution.
Li SC, Chan WC, Lai CH, Tsai KW, Hsu CN, Jou YS, Chen HC, Chen CH, Lin WC., BMC Bioinformatics 12 Suppl 1(), 2011
PMID: 21342592
Li SC, Chan WC, Lai CH, Tsai KW, Hsu CN, Jou YS, Chen HC, Chen CH, Lin WC., BMC Bioinformatics 12 Suppl 1(), 2011
PMID: 21342592
Mixture models for analysis of the taxonomic composition of metagenomes.
Meinicke P, Asshauer KP, Lingner T., Bioinformatics 27(12), 2011
PMID: 21546400
Meinicke P, Asshauer KP, Lingner T., Bioinformatics 27(12), 2011
PMID: 21546400
Taxonomic classification of metagenomic shotgun sequences with CARMA3.
Gerlach W, Stoye J., Nucleic Acids Res 39(14), 2011
PMID: 21586583
Gerlach W, Stoye J., Nucleic Acids Res 39(14), 2011
PMID: 21586583
CoMet--a web server for comparative functional profiling of metagenomes.
Lingner T, Asshauer KP, Schreiber F, Meinicke P., Nucleic Acids Res 39(web server issue), 2011
PMID: 21622656
Lingner T, Asshauer KP, Schreiber F, Meinicke P., Nucleic Acids Res 39(web server issue), 2011
PMID: 21622656
Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii.
Ghamsari L, Balaji S, Shen Y, Yang X, Balcha D, Fan C, Hao T, Yu H, Papin JA, Salehi-Ashtiani K., BMC Genomics 12 Suppl 1(), 2011
PMID: 21810206
Ghamsari L, Balaji S, Shen Y, Yang X, Balcha D, Fan C, Hao T, Yu H, Papin JA, Salehi-Ashtiani K., BMC Genomics 12 Suppl 1(), 2011
PMID: 21810206
Integrative analysis of environmental sequences using MEGAN4.
Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC., Genome Res 21(9), 2011
PMID: 21690186
Huson DH, Mitra S, Ruscheweyh HJ, Weber N, Schuster SC., Genome Res 21(9), 2011
PMID: 21690186
Accurate and fast estimation of taxonomic profiles from metagenomic shotgun sequences.
Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M., BMC Genomics 12 Suppl 2(), 2011
PMID: 21989143
Liu B, Gibbons T, Ghodsi M, Treangen T, Pop M., BMC Genomics 12 Suppl 2(), 2011
PMID: 21989143
Comparison of statistical methods to classify environmental genomic fragments.
Rosen GL, Essinger SD., IEEE Trans Nanobioscience 9(4), 2010
PMID: 20876033
Rosen GL, Essinger SD., IEEE Trans Nanobioscience 9(4), 2010
PMID: 20876033
Clustering metagenomic sequences with interpolated Markov models.
Kelley DR, Salzberg SL., BMC Bioinformatics 11(), 2010
PMID: 21044341
Kelley DR, Salzberg SL., BMC Bioinformatics 11(), 2010
PMID: 21044341
38 References
Daten bereitgestellt von Europe PubMed Central.
The Pfam protein families database.
Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A., Nucleic Acids Res. 36(Database issue), 2008
PMID: 18039703
Finn RD, Tate J, Mistry J, Coggill PC, Sammut SJ, Hotz HR, Ceric G, Forslund K, Eddy SR, Sonnhammer EL, Bateman A., Nucleic Acids Res. 36(Database issue), 2008
PMID: 18039703
AUTHOR UNKNOWN, 2002
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Saitou N, Nei M., Mol. Biol. Evol. 4(4), 1987
PMID: 3447015
Saitou N, Nei M., Mol. Biol. Evol. 4(4), 1987
PMID: 3447015
Gene ontology: tool for the unification of biology. The Gene Ontology Consortium.
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., Nat. Genet. 25(1), 2000
PMID: 10802651
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., Nat. Genet. 25(1), 2000
PMID: 10802651
Database resources of the National Center for Biotechnology Information.
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., Nucleic Acids Res. 37(Database issue), 2009
PMID: 18940862
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., Nucleic Acids Res. 37(Database issue), 2009
PMID: 18940862
NCBI Taxonomy Statistics
AUTHOR UNKNOWN, 0
AUTHOR UNKNOWN, 0
PHYLIP - Phylogeny Inference Package (Version 3.2)
AUTHOR UNKNOWN, 1989
AUTHOR UNKNOWN, 1989
The metagenome of a biogas-producing microbial community of a production-scale biogas plant fermenter analysed by the 454-pyrosequencing technology.
Schluter A, Bekel T, Diaz NN, Dondrup M, Eichenlaub R, Gartemann KH, Krahn I, Krause L, Kromeke H, Kruse O, Mussgnug JH, Neuweger H, Niehaus K, Puhler A, Runte KJ, Szczepanowski R, Tauch A, Tilker A, Viehover P, Goesmann A., J. Biotechnol. 136(1-2), 2008
PMID: 18597880
Schluter A, Bekel T, Diaz NN, Dondrup M, Eichenlaub R, Gartemann KH, Krahn I, Krause L, Kromeke H, Kruse O, Mussgnug JH, Neuweger H, Niehaus K, Puhler A, Runte KJ, Szczepanowski R, Tauch A, Tilker A, Viehover P, Goesmann A., J. Biotechnol. 136(1-2), 2008
PMID: 18597880
Accurate whole human genome sequencing using reversible terminator chemistry.
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, Keira Cheetham R, 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 IM, 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 DM, 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, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, 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, Huw Jones TA, 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, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, 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, Ernest Sohna Sohna J, 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., Nature 456(7218), 2008
PMID: 18987734
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, Keira Cheetham R, 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 IM, 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 DM, 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, Chiara E Catenazzi M, Chang S, Neil Cooley R, Crake NR, Dada OO, Diakoumakos KD, Dominguez-Fernandez B, Earnshaw DJ, Egbujor UC, Elmore DW, Etchin SS, Ewan MR, Fedurco M, Fraser LJ, Fuentes Fajardo KV, Scott Furey W, 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, Huw Jones TA, 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, Ling Ng B, Novo SM, O'Neill MJ, Osborne MA, Osnowski A, Ostadan O, Paraschos LL, Pickering L, Pike AC, Pike AC, Chris Pinkard D, Pliskin DP, Podhasky J, Quijano VJ, Raczy C, Rae VH, Rawlings SR, Chiva Rodriguez A, Roe PM, Rogers J, Rogert Bacigalupo MC, 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, Ernest Sohna Sohna J, 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., Nature 456(7218), 2008
PMID: 18987734
Substantial biases in ultra-short read data sets from high-throughput DNA sequencing.
Dohm JC, Lottaz C, Borodina T, Himmelbauer H., Nucleic Acids Res. 36(16), 2008
PMID: 18660515
Dohm JC, Lottaz C, Borodina T, Himmelbauer H., Nucleic Acids Res. 36(16), 2008
PMID: 18660515
Characterizing the mouse ES cell transcriptome with Illumina sequencing.
Rosenkranz R, Borodina T, Lehrach H, Himmelbauer H., Genomics 92(4), 2008
PMID: 18602984
Rosenkranz R, Borodina T, Lehrach H, Himmelbauer H., Genomics 92(4), 2008
PMID: 18602984
Export
Markieren/ Markierung löschen
Markierte Publikationen
Web of Science
Dieser Datensatz im Web of Science®Quellen
PMID: 20021646
PubMed | Europe PMC
Suchen in
Google Scholar