V-Xtractor: An open-source, high-throughput software tool to identify and extract hypervariable regions of small subunit (16 S/18 S) ribosomal RNA gene sequences

被引：92

作者：

Hartmann, Martin ^{[1
]}

Howes, Charles G. ^{[1
]}

Abarenkov, Kessy ^{[2
]}

Mohn, William W. ^{[1
]}

Nilsson, R. Henrik ^{[2
,3
]}

机构：

[1] Univ British Columbia, Dept Microbiol & Immunol, Inst Life Sci, Vancouver, BC V5Z 1M9, Canada

[2] Univ Tartu, Dept Bot, Inst Ecol & Earth Sci, EE-50090 Tartu, Estonia

[3] Univ Gothenburg, Dept Plant & Environm Sci, Gothenburg, Sweden

来源：

JOURNAL OF MICROBIOLOGICAL METHODS | 2010年 / 83卷 / 02期

关键词：

Software; SSU rRNA sequences; Hypervariable regions; High-throughput sequencing; Hidden Markov Models; HMMER; COMMUNITIES; DATABASE; GENERATION; SPACE; SEA; ARB;

D O I：

10.1016/j.mimet.2010.08.008

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

V-Xtractor (http://www.cmde.science.ubc.ca/mohn/software.html) uses Hidden Markov Models to locate, verify, and extract defined hypervariable sequence segments (V1-V9) from bacterial, archaeal, and fungal small-subunit rRNA sequences. With a detection efficiency of 99.6% and low susceptibility to false-positives, this tool refines data reliability and facilitates subsequent analysis in community assays. (C) 2010 Elsevier B.V. All rights reserved.

引用

页码：250 / 253

页数：4

共 17 条

[1] Gapped BLAST and PSI-BLAST: a new generation of protein database search programs [J].

Altschul, SF ;

Madden, TL ;

Schaffer, AA ;

Zhang, JH ;

Zhang, Z ;

Miller, W ;

Lipman, DJ .

NUCLEIC ACIDS RESEARCH, 1997, 25 (17) :3389-3402

[2] Pyrosequencing reveals contrasting seasonal dynamics of taxa within Baltic Sea bacterioplankton communities [J].

Andersson, Anders F. ;

Riemann, Lasse ;

Bertilsson, Stefan .

ISME JOURNAL, 2010, 4 (02) :171-181

[3] Biodiversity: Something new under the sea [J].

Boucher, Y ;

Doolittle, WF .

NATURE, 2002, 417 (6884) :27-28

[4] The ribosomal database project (RDP-II): introducing myRDP space and quality controlled public data [J].

Cole, J. R. ;

Chai, B. ;

Farris, R. J. ;

Wang, Q. ;

Kulam-Syed-Mohideen, A. S. ;

McGarrell, D. M. ;

Bandela, A. M. ;

Cardenas, E. ;

Garrity, G. M. ;

Tiedje, J. M. .

NUCLEIC ACIDS RESEARCH, 2007, 35 :D169-D172

[5] Greengenes, a chimera-checked 16S rRNA gene database and workbench compatible with ARB [J].

DeSantis, T. Z. ;

Hugenholtz, P. ;

Larsen, N. ;

Rojas, M. ;

Brodie, E. L. ;

Keller, K. ;

Huber, T. ;

Dalevi, D. ;

Hu, P. ;

Andersen, G. L. .

APPLIED AND ENVIRONMENTAL MICROBIOLOGY, 2006, 72 (07) :5069-5072

[6] Profile hidden Markov models [J].

Eddy, SR .

BIOINFORMATICS, 1998, 14 (09) :755-763

[7] Bacterial communities of disease vectors sampled across time, space, and species [J].

Jones, Ryan T. ;

Knight, Rob ;

Martin, Andrew P. .

ISME JOURNAL, 2010, 4 (02) :223-231

[8] Metagenomic study of the oral microbiota by Illumina high-throughput sequencing [J].

Lazarevic, Vladimir ;

Whiteson, Katrine ;

Huse, Susan ;

Hernandez, David ;

Farinelli, Laurent ;

Osteras, Magne ;

Schrenzel, Jacques ;

Francois, Patrice .

JOURNAL OF MICROBIOLOGICAL METHODS, 2009, 79 (03) :266-271

[9] Genome sequencing in microfabricated high-density picolitre reactors [J].

Margulies, M ;

Egholm, M ;

Altman, WE ;

Attiya, S ;

Bader, JS ;

Bemben, LA ;

Berka, J ;

Braverman, MS ;

Chen, YJ ;

Chen, ZT ;

Dewell, SB ;

Du, L ;

Fierro, JM ;

Gomes, XV ;

Godwin, BC ;

He, W ;

Helgesen, S ;

Ho, CH ;

Irzyk, GP ;

Jando, SC ;

Alenquer, MLI ;

Jarvie, TP ;

Jirage, KB ;

Kim, JB ;

Knight, JR ;

Lanza, JR ;

Leamon, JH ;

Lefkowitz, SM ;

Lei, M ;

Li, J ;

Lohman, KL ;

Lu, H ;

Makhijani, VB ;

McDade, KE ;

McKenna, MP ;

Myers, EW ;

Nickerson, E ;

Nobile, JR ;

Plant, R ;

Puc, BP ;

Ronan, MT ;

Roth, GT ;

Sarkis, GJ ;

Simons, JF ;

Simpson, JW ;

Srinivasan, M ;

Tartaro, KR ;

Tomasz, A ;

Vogt, KA ;

Volkmer, GA .

NATURE, 2005, 437 (7057) :376-380

[10] An open source software package for automated extraction of ITS1 and ITS2 from fungal ITS sequences for use in high-throughput community assays and molecular ecology [J].

Nilsson, R. Henrik ;

Veldre, Vilmar ;

Hartmann, Martin ;

Unterseher, Martin ;

Amend, Anthony ;

Bergsten, Johannes ;

Kristiansson, Erik ;

Ryberg, Martin ;

Jumpponen, Ari ;

Abarenkov, Kessy .

FUNGAL ECOLOGY, 2010, 3 (04) :284-287

← 1 2 →