Ultrafast clustering algorithms for metagenomic sequence analysis

The rapid advances of high-throughput sequencing technologies dramatically prompted metagenomic studies of microbial communities that exist at various environments. Fundamental questions in metagenomics include the identities, composition and dynamics of microbial populations and their functions and...

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Vydáno v:	Briefings in bioinformatics Ročník 13; číslo 6; s. 656 - 668
Hlavní autoři:	Li, W., Fu, L., Niu, B., Wu, S., Wooley, J.
Médium:	Journal Article
Jazyk:	angličtina
Vydáno:	England Oxford Publishing Limited (England) 01.11.2012 Oxford University Press
Témata:	Algorithms Bioinformatics Cluster Analysis Data analysis Errors Genomics Metagenome Metagenomics Microbial activity Microbiology Sequence Analysis, DNA
ISSN:	1467-5463, 1477-4054, 1477-4054
On-line přístup:	Získat plný text
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Abstract	The rapid advances of high-throughput sequencing technologies dramatically prompted metagenomic studies of microbial communities that exist at various environments. Fundamental questions in metagenomics include the identities, composition and dynamics of microbial populations and their functions and interactions. However, the massive quantity and the comprehensive complexity of these sequence data pose tremendous challenges in data analysis. These challenges include but are not limited to ever-increasing computational demand, biased sequence sampling, sequence errors, sequence artifacts and novel sequences. Sequence clustering methods can directly answer many of the fundamental questions by grouping similar sequences into families. In addition, clustering analysis also addresses the challenges in metagenomics. Thus, a large redundant data set can be represented with a small non-redundant set, where each cluster can be represented by a single entry or a consensus. Artifacts can be rapidly detected through clustering. Errors can be identified, filtered or corrected by using consensus from sequences within clusters.
AbstractList	The rapid advances of high-throughput sequencing technologies dramatically prompted metagenomic studies of microbial communities that exist at various environments. Fundamental questions in metagenomics include the identities, composition and dynamics of microbial populations and their functions and interactions. However, the massive quantity and the comprehensive complexity of these sequence data pose tremendous challenges in data analysis. These challenges include but are not limited to ever-increasing computational demand, biased sequence sampling, sequence errors, sequence artifacts and novel sequences. Sequence clustering methods can directly answer many of the fundamental questions by grouping similar sequences into families. In addition, clustering analysis also addresses the challenges in metagenomics. Thus, a large redundant data set can be represented with a small non-redundant set, where each cluster can be represented by a single entry or a consensus. Artifacts can be rapidly detected through clustering. Errors can be identified, filtered or corrected by using consensus from sequences within clusters. The rapid advances of high-throughput sequencing technologies dramatically prompted metagenomic studies of microbial communities that exist at various environments. Fundamental questions in metagenomics include the identities, composition and dynamics of microbial populations and their functions and interactions. However, the massive quantity and the comprehensive complexity of these sequence data pose tremendous challenges in data analysis. These challenges include but are not limited to ever-increasing computational demand, biased sequence sampling, sequence errors, sequence artifacts and novel sequences. Sequence clustering methods can directly answer many of the fundamental questions by grouping similar sequences into families. In addition, clustering analysis also addresses the challenges in metagenomics. Thus, a large redundant data set can be represented with a small non-redundant set, where each cluster can be represented by a single entry or a consensus. Artifacts can be rapidly detected through clustering. Errors can be identified, filtered or corrected by using consensus from sequences within clusters.The rapid advances of high-throughput sequencing technologies dramatically prompted metagenomic studies of microbial communities that exist at various environments. Fundamental questions in metagenomics include the identities, composition and dynamics of microbial populations and their functions and interactions. However, the massive quantity and the comprehensive complexity of these sequence data pose tremendous challenges in data analysis. These challenges include but are not limited to ever-increasing computational demand, biased sequence sampling, sequence errors, sequence artifacts and novel sequences. Sequence clustering methods can directly answer many of the fundamental questions by grouping similar sequences into families. In addition, clustering analysis also addresses the challenges in metagenomics. Thus, a large redundant data set can be represented with a small non-redundant set, where each cluster can be represented by a single entry or a consensus. Artifacts can be rapidly detected through clustering. Errors can be identified, filtered or corrected by using consensus from sequences within clusters. The rapid advances of high-throughput sequencing technologies dramatically prompted metagenomic studies of microbial communities that exist at various environments. Fundamental questions in metagenomics include the identities, composition and dynamics of microbial populations and their functions and interactions. However, the massive quantity and the comprehensive complexity of these sequence data pose tremendous challenges in data analysis. These challenges include but are not limited to ever-increasing computational demand, biased sequence sampling, sequence errors, sequence artifacts and novel sequences. Sequence clustering methods can directly answer many of the fundamental questions by grouping similar sequences into families. In addition, clustering analysis also addresses the challenges in metagenomics. Thus, a large redundant data set can be represented with a small non-redundant set, where each cluster can be represented by a single entry or a consensus. Artifacts can be rapidly detected through clustering. Errors can be identified, filtered or corrected by using consensus from sequences within clusters. [PUBLICATION ABSTRACT]
Author	Niu, B. Li, W. Fu, L. Wooley, J. Wu, S.
Author_xml	– sequence: 1 givenname: W. surname: Li fullname: Li, W. – sequence: 2 givenname: L. surname: Fu fullname: Fu, L. – sequence: 3 givenname: B. surname: Niu fullname: Niu, B. – sequence: 4 givenname: S. surname: Wu fullname: Wu, S. – sequence: 5 givenname: J. surname: Wooley fullname: Wooley, J.
BackLink	https://www.ncbi.nlm.nih.gov/pubmed/22772836$$D View this record in MEDLINE/PubMed
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Cites_doi	10.1093/bioinformatics/18.1.77 10.1101/gr.097261.109 10.1093/nar/gkg096 10.1371/journal.pbio.0050077 10.1101/gr.229202. Article published online before March 2002 10.1111/j.1462-2920.2009.02051.x 10.1093/bioinformatics/btg034 10.1093/bioinformatics/btq003 10.1038/nature07540 10.1093/bioinformatics/btn174 10.1093/nar/gkq1102 10.1038/nmeth.1361 10.1038/nbt.1966 10.1126/science.1093857 10.1093/bioinformatics/btp336 10.1186/1471-2105-9-182 10.1126/science.1124234 10.1186/1471-2105-12-38 10.1038/nature08821 10.1093/bioinformatics/17.3.282 10.1093/bioinformatics/btg138 10.1038/nature09796 10.1186/1471-2105-10-359 10.1093/nar/gkn879 10.1093/bioinformatics/16.5.451 10.1371/journal.pbio.0050016 10.1371/journal.pone.0003042 10.1093/bioinformatics/btr208 10.1126/science.1200387 10.1093/nar/27.1.29 10.1038/nmeth.f.303 10.1110/ps.9.2.232 10.1093/nar/gkg620 10.1038/ng0895-369 10.1093/nar/gkp985 10.1089/cmb.2010.0127 10.1186/1471-2105-12-159 10.1093/bioinformatics/btr252 10.1093/bioinformatics/btp324 10.1101/gr.096651.109 10.1126/science.1177486 10.1093/nar/gkl723 10.1128/MMBR.68.4.669-685.2004 10.1093/nar/25.17.3389 10.1128/AEM.01541-09 10.1093/bib/bbr009 10.1101/gr.074492.107 10.1093/bioinformatics/btq461 10.1093/nar/30.7.1575 10.1093/bioinformatics/18.1.182 10.1101/gr.111351.110 10.1093/nar/gkm869 10.1126/science.1107851 10.1038/ismej.2009.72 10.1093/nar/gkp285 10.1093/bioinformatics/16.5.458 10.1093/bioinformatics/btl158 10.1093/protein/15.8.643 10.1093/bioinformatics/btr560 10.1101/gr.089151.108 10.1101/gr.1224503 10.1186/1471-2105-11-187 10.1371/journal.pcbi.1000667 10.1186/1471-2105-12-271 10.1186/1471-2164-12-444 10.1128/AEM.71.3.1501-1506.2005 10.1093/nar/gkm864 10.1186/1471-2105-9-386 10.1093/nar/28.1.49 10.1371/journal.pone.0003375 10.1111/j.1462-2920.2010.02193.x 10.1038/nmeth0910-668b 10.1093/bioinformatics/btm098 10.1128/AEM.03006-05 10.1101/gr.9.11.1135 10.1093/bioinformatics/btr447 10.1038/nature06810
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References	(38_27960295) 2007; 23 Hess (8_39040974) 2011; 331 Ghodsi (40_40258483) 2011; 12 (62_34993581) 2009; 25 Schloss (49_18715428) 2005; 71 Meyer (45_32006915) 2008; 9 (51_34732864) 2009; 37 Quince (56_39155534) 2011; 12 Kunin (53_35537372) 2010; 12 DeSantis (72_22337314) 2006; 72 Li (76_35888349) 2009; 10 Pertea (33_17550109) 2003; 19 (66_20030001) 2002; 12 (79_38180305) 2009; 23 (44_35911179) 2009; 326 (41_40451192) 2011; 27 (63_30650833) 2008; 18 Mardis (6_39216581) 2011; 470 Reeder (55_38032744) 2010; 7 (78_35997997) 2010; 38 Sasson (19_17466558) 2003; 31 Park (20_10370229) 2000; 16 Handelsman (1_18563789) 2004; 68 Yooseph (16_27939021) 2007; 5 Ye (68_39957809) 2011; 12 Zhao (59_38399386) 2010; 17 (71_32600541) 2009; 37 (50_39800292) 2012; 13 Huse (52_36898660) 2010; 12 (14_35682275) 2009; 75 (73_37744994) 1999; 27 Rychlewski (74_6507520) 2000; 9 Chitsaz (11_40802876) 2011; 29 (64_36199899) 2010; 20 Malde (35_17699328) 2003; 19 (27_37723758) 1997; 25 (65_34872029) 2009; 25 Dinsdale (7_30759130) 2008; 452 Li (25_17795155) 2003; 13 (42_38471862) 2011; 39 Enright (21_10370228) 2000; 16 Gilbert (17_31784553) 2008; 3 (3_18125245) 2004; 304 Wu (43_40734695) 2011; 12 Pipenbacher (23_18339069) 2002; 18 Yona (18_6399185) 2000; 28 (28_36294183) 2010; 26 (48_43007872) 2009; 457 (61_39688836) 2011; 21 Gill (4_22205791) 2006; 312 Tringe (5_18820502) 2005; 308 (46_29606269) 2008; 36 Gomez-Alvarez (12_35262564) 2009; 3 (39_37901752) 2010; 26 Li (15_32164888) 2008; 3 (60_40138237) 2011; 27 Burke (34_6374359) 1999; 9 (37_40952907) 2011; 27 Boguski (32_16004542) 1995; 10 (58_34822443) 2009; 19 (29_22189101) 2006; 22 Li (69_17269867) 2002; 15 (26_31321771) 2008; 24 (67_39738118) 2011; 27 (70_29729501) 2007; 35 Li (31_16908259) 2002; 18 (36_27102599) 2005; 6 Niu (13_37108173) 2010; 11 Wooley (2_36737560) 2010; 6 Mika (24_17690859) 2003; 31 Caporaso (57_37096338) 2010; 7 (10_35731688) 2009; 19 Enright (22_16978057) 2002; 30 Quince (54_35448469) 2009; 6 Li (30_11106110) 2001; 17 Yooseph (75_30826533) 2008; 9 Qin (9_36747651) 2010; 464 Rusch (47_27939026) 2007; 5 (77_22767648) 2006; 34 20709691 - Bioinformatics. 2010 Oct 1;26(19):2460-1 19668203 - Nat Methods. 2009 Sep;6(9):639-41 18337718 - Nature. 2008 Apr 3;452(7187):629-32 19863816 - BMC Bioinformatics. 2009;10:359 10716175 - Protein Sci. 2000 Feb;9(2):232-41 21276213 - BMC Bioinformatics. 2011;12:38 10568753 - Genome Res. 1999 Nov;9(11):1135-42 17932063 - Nucleic Acids Res. 2008 Jan;36(Database issue):D534-8 11917018 - Nucleic Acids Res. 2002 Apr 1;30(7):1575-84 12386002 - Bioinformatics. 2002;18 Suppl 2:S182-91 12824419 - Nucleic Acids Res. 2003 Jul 1;31(13):3789-91 21045053 - Nucleic Acids Res. 2011 Jan;39(Database issue):D546-51 21984769 - Bioinformatics. 2011 Dec 15;27(24):3348-55 19043404 - Nature. 2009 Jan 22;457(7228):480-4 19417062 - Nucleic Acids Res. 2009 Jun;37(10):e76 21307932 - Nature. 2011 Feb 10;470(7333):198-203 19920124 - Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22 21273488 - Science. 2011 Jan 28;331(6016):463-7 21685062 - Bioinformatics. 2011 Jul 1;27(13):i137-41 21926975 - Nat Biotechnol. 2011 Oct;29(10):915-21 7670480 - Nat Genet. 1995 Aug;10(4):369-71 16026600 - BMC Bioinformatics. 2005;6 Suppl 2:S3 18803844 - BMC Bioinformatics. 2008;9:386 11294794 - Bioinformatics. 2001 Mar;17(3):282-3 21718538 - BMC Bioinformatics. 2011;12:271 9254694 - Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 21899761 - BMC Genomics. 2011;12:444 19497933 - Bioinformatics. 2009 Aug 1;25(15):1966-7 21810899 - Bioinformatics. 2011 Sep 15;27(18):2502-9 20388221 - BMC Bioinformatics. 2010;11:187 19892944 - Science. 2009 Dec 18;326(5960):1694-7 20203603 - Nature. 2010 Mar 4;464(7285):59-65 19819907 - Genome Res. 2009 Dec;19(12):2317-23 16820507 - Appl Environ Microbiol. 2006 Jul;72(7):5069-72 21505035 - Bioinformatics. 2011 Jun 15;27(12):1704-5 15590779 - Microbiol Mol Biol Rev. 2004 Dec;68(4):669-85 15001713 - Science. 2004 Apr 2;304(5667):66-74 12952885 - Genome Res. 2003 Sep;13(9):2178-89 15746353 - Appl Environ Microbiol. 2005 Mar;71(3):1501-6 17028096 - Nucleic Acids Res. 2006;34(19):5623-30 11932250 - Genome Res. 2002 Apr;12(4):656-64 19439514 - Genome Res. 2009 Jul;19(7):1309-15 18402669 - BMC Bioinformatics. 2008;9:182 18846219 - PLoS One. 2008;3(10):e3375 11836214 - Bioinformatics. 2002 Jan;18(1):77-82 19451168 - Bioinformatics. 2009 Jul 15;25(14):1754-60 18586742 - Bioinformatics. 2008 Jul 1;24(13):i41-9 21525143 - Brief Bioinform. 2012 Jan;13(1):107-21 20195499 - PLoS Comput Biol. 2010 Feb;6(2):e1000667 21482625 - Genome Res. 2011 Jul;21(7):1181-92 20383131 - Nat Methods. 2010 May;7(5):335-6 17355176 - PLoS Biol. 2007 Mar;5(3):e77 20973743 - J Comput Biol. 2010 Nov;17(11):1549-60 12364578 - Protein Eng. 2002 Aug;15(8):643-9 16731699 - Bioinformatics. 2006 Jul 1;22(13):1658-9 9847135 - Nucleic Acids Res. 1999 Jan 1;27(1):29-34 17947321 - Nucleic Acids Res. 2007;35(21):7188-96 19004872 - Nucleic Acids Res. 2009 Jan;37(Database issue):D141-5 20053844 - Bioinformatics. 2010 Mar 1;26(5):680-2 20019144 - Genome Res. 2010 Feb;20(2):265-72 12835265 - Bioinformatics. 2003 Jul 1;19(10):1221-6 18725995 - PLoS One. 2008;3(8):e3042 19725865 - Environ Microbiol. 2010 Jan;12(1):118-23 19801464 - Appl Environ Microbiol. 2009 Dec;75(23):7537-41 21575167 - BMC Bioinformatics. 2011;12:159 10871268 - Bioinformatics. 2000 May;16(5):458-64 10871267 - Bioinformatics. 2000 May;16(5):451-7 17355171 - PLoS Biol. 2007 Mar;5(3):e16 10592179 - Nucleic Acids Res. 2000 Jan 1;28(1):49-55 12520020 - Nucleic Acids Res. 2003 Jan 1;31(1):348-52 20180275 - Genome Inform. 2009 Oct;23(1):205-11 15845853 - Science. 2005 Apr 22;308(5721):554-7 18349386 - Genome Res. 2008 May;18(5):821-9 17379688 - Bioinformatics. 2007 May 15;23(10):1282-8 19587772 - ISME J. 2009 Nov;3(11):1314-7 20805793 - Nat Methods. 2010 Sep;7(9):668-9 12651724 - Bioinformatics. 2003 Mar 22;19(5):651-2 20236171 - Environ Microbiol. 2010 Jul;12(7):1889-98 16741115 - Science. 2006 Jun 2;312(5778):1355-9
References_xml	– volume: 18 start-page: 77 issn: 1367-4803 issue: 1 year: 2002 ident: 31_16908259 publication-title: Bioinformatics doi: 10.1093/bioinformatics/18.1.77 – volume: 20 start-page: 265 issn: 1088-9051 issue: 2 year: 2010 ident: 64_36199899 publication-title: Genome Research doi: 10.1101/gr.097261.109 – volume: 31 start-page: 348 issn: 0305-1048 issue: 1 year: 2003 ident: 19_17466558 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkg096 – volume: 5 start-page: e77 issn: 1544-9173 issue: 3 year: 2007 ident: 47_27939026 publication-title: PLoS biology doi: 10.1371/journal.pbio.0050077 – volume: 12 start-page: 656 issn: 1088-9051 issue: 4 year: 2002 ident: 66_20030001 publication-title: Genome Research doi: 10.1101/gr.229202. Article published online before March 2002 – volume: 12 start-page: 118 issn: 1462-2920 issue: 1 year: 2010 ident: 53_35537372 publication-title: Environmental Microbiology (Print) doi: 10.1111/j.1462-2920.2009.02051.x – volume: 19 start-page: 651 issn: 1367-4803 issue: 5 year: 2003 ident: 33_17550109 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btg034 – volume: 26 start-page: 680 issn: 1367-4803 issue: 5 year: 2010 ident: 28_36294183 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq003 – volume: 457 start-page: U480 issn: 1476-4687 year: 2009 ident: 48_43007872 publication-title: Nature; Physical Science (London) doi: 10.1038/nature07540 – volume: 24 start-page: i41 issn: 1367-4803 issue: 13 year: 2008 ident: 26_31321771 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btn174 – volume: 39 start-page: D546 issn: 0305-1048 issue: suppl_1 year: 2011 ident: 42_38471862 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkq1102 – volume: 6 start-page: 639 issn: 1548-7091 issue: 9 year: 2009 ident: 54_35448469 doi: 10.1038/nmeth.1361 – volume: 29 start-page: 915 issn: 1087-0156 issue: 10 year: 2011 ident: 11_40802876 publication-title: Nature biotechnology doi: 10.1038/nbt.1966 – volume: 304 start-page: 66 issn: 0036-8075 issue: 5667 year: 2004 ident: 3_18125245 publication-title: Science doi: 10.1126/science.1093857 – volume: 25 start-page: 1966 issn: 1367-4803 issue: 15 year: 2009 ident: 62_34993581 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp336 – volume: 9 start-page: 182 issn: 1471-2105 year: 2008 ident: 75_30826533 publication-title: BMC bioinformatics [electronic resource] doi: 10.1186/1471-2105-9-182 – volume: 312 start-page: 1355 issn: 0036-8075 issue: 5778 year: 2006 ident: 4_22205791 publication-title: Science doi: 10.1126/science.1124234 – volume: 12 start-page: 38 issn: 1471-2105 year: 2011 ident: 56_39155534 publication-title: BMC bioinformatics [electronic resource] doi: 10.1186/1471-2105-12-38 – volume: 464 start-page: 59 issn: 1476-4687 issue: 7285 year: 2010 ident: 9_36747651 publication-title: Nature; Physical Science (London) doi: 10.1038/nature08821 – volume: 17 start-page: 282 issn: 1367-4803 issue: 3 year: 2001 ident: 30_11106110 publication-title: Bioinformatics doi: 10.1093/bioinformatics/17.3.282 – volume: 19 start-page: 1221 issn: 1367-4803 issue: 10 year: 2003 ident: 35_17699328 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btg138 – volume: 23 start-page: 205 year: 2009 ident: 79_38180305 publication-title: GENOME INFORM – volume: 470 start-page: 198 issn: 1476-4687 issue: 7333 year: 2011 ident: 6_39216581 publication-title: Nature; Physical Science (London) doi: 10.1038/nature09796 – volume: 10 start-page: 359 issn: 1471-2105 year: 2009 ident: 76_35888349 publication-title: BMC bioinformatics [electronic resource] doi: 10.1186/1471-2105-10-359 – volume: 37 start-page: D141 issn: 0305-1048 issue: suppl_1 year: 2009 ident: 71_32600541 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkn879 – volume: 16 start-page: 451 issn: 1367-4803 issue: 5 year: 2000 ident: 21_10370228 publication-title: Bioinformatics doi: 10.1093/bioinformatics/16.5.451 – volume: 5 start-page: e16 issn: 1544-9173 issue: 3 year: 2007 ident: 16_27939021 publication-title: PLoS biology doi: 10.1371/journal.pbio.0050016 – volume: 3 start-page: e3042 issn: 1932-6203 issue: 8 year: 2008 ident: 17_31784553 doi: 10.1371/journal.pone.0003042 – volume: 27 start-page: i137 issn: 1367-4803 issue: 13 year: 2011 ident: 60_40138237 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr208 – volume: 331 start-page: 463 issn: 0036-8075 issue: 6016 year: 2011 ident: 8_39040974 publication-title: Science doi: 10.1126/science.1200387 – volume: 27 start-page: 29 issn: 0305-1048 issue: 1 year: 1999 ident: 73_37744994 publication-title: Nucleic Acids Research doi: 10.1093/nar/27.1.29 – volume: 7 start-page: 335 issn: 1548-7091 issue: 5 year: 2010 ident: 57_37096338 doi: 10.1038/nmeth.f.303 – volume: 9 start-page: 232 issn: 0961-8368 issue: 2 year: 2000 ident: 74_6507520 publication-title: Protein Science doi: 10.1110/ps.9.2.232 – volume: 31 start-page: 3789 issn: 0305-1048 issue: 13 year: 2003 ident: 24_17690859 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkg620 – volume: 10 start-page: 369 issn: 1061-4036 issue: 4 year: 1995 ident: 32_16004542 publication-title: Nature genetics doi: 10.1038/ng0895-369 – volume: 38 start-page: D211 issn: 0305-1048 issue: suppl_1 year: 2010 ident: 78_35997997 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkp985 – volume: 17 start-page: 1549 issn: 1066-5277 issue: 11 year: 2010 ident: 59_38399386 publication-title: Journal of computational biology : a journal of computational molecular cell biology doi: 10.1089/cmb.2010.0127 – volume: 12 start-page: 159 issn: 1471-2105 year: 2011 ident: 68_39957809 publication-title: BMC bioinformatics [electronic resource] doi: 10.1186/1471-2105-12-159 – volume: 27 start-page: 1704 issn: 1367-4803 issue: 12 year: 2011 ident: 67_39738118 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr252 – volume: 25 start-page: 1754 issn: 1367-4803 issue: 14 year: 2009 ident: 65_34872029 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btp324 – volume: 19 start-page: 2317 issn: 1088-9051 issue: 12 year: 2009 ident: 10_35731688 publication-title: Genome Research doi: 10.1101/gr.096651.109 – volume: 326 start-page: 1694 issn: 0036-8075 issue: 5960 year: 2009 ident: 44_35911179 publication-title: Science doi: 10.1126/science.1177486 – volume: 34 start-page: 5623 issn: 0305-1048 issue: 19 year: 2006 ident: 77_22767648 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkl723 – volume: 68 start-page: 669 issn: 1092-2172 issue: 4 year: 2004 ident: 1_18563789 publication-title: Microbiology and Molecular Biology Reviews doi: 10.1128/MMBR.68.4.669-685.2004 – volume: 25 start-page: 3389 issn: 0305-1048 issue: 17 year: 1997 ident: 27_37723758 publication-title: Nucleic Acids Research doi: 10.1093/nar/25.17.3389 – volume: 75 start-page: 7537 issn: 0099-2240 issue: 23 year: 2009 ident: 14_35682275 publication-title: Applied and Environmental Microbiology doi: 10.1128/AEM.01541-09 – volume: 13 start-page: 107 issn: 1467-5463 issue: 1 year: 2012 ident: 50_39800292 publication-title: Briefings in Bioinformatics doi: 10.1093/bib/bbr009 – volume: 18 start-page: 821 issn: 1088-9051 issue: 5 year: 2008 ident: 63_30650833 publication-title: Genome Research doi: 10.1101/gr.074492.107 – volume: 26 start-page: 2460 issn: 1367-4803 issue: 19 year: 2010 ident: 39_37901752 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btq461 – volume: 30 start-page: 1575 issn: 0305-1048 issue: 7 year: 2002 ident: 22_16978057 publication-title: Nucleic Acids Research doi: 10.1093/nar/30.7.1575 – volume: 18 start-page: S182 issn: 1367-4803 issue: 90002 year: 2002 ident: 23_18339069 publication-title: Bioinformatics doi: 10.1093/bioinformatics/18.1.182 – volume: 21 start-page: 1181 issn: 1088-9051 issue: 7 year: 2011 ident: 61_39688836 publication-title: Genome Research doi: 10.1101/gr.111351.110 – volume: 36 start-page: D534 issn: 0305-1048 issue: suppl_1 year: 2008 ident: 46_29606269 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkm869 – volume: 308 start-page: 554 issn: 0036-8075 issue: 5721 year: 2005 ident: 5_18820502 publication-title: Science doi: 10.1126/science.1107851 – volume: 3 start-page: 1314 issn: 1751-7362 issue: 11 year: 2009 ident: 12_35262564 doi: 10.1038/ismej.2009.72 – volume: 37 start-page: e76 issn: 0305-1048 issue: 10 year: 2009 ident: 51_34732864 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkp285 – volume: 16 start-page: 458 issn: 1367-4803 issue: 5 year: 2000 ident: 20_10370229 publication-title: Bioinformatics doi: 10.1093/bioinformatics/16.5.458 – volume: 22 start-page: 1658 issn: 1367-4803 issue: 13 year: 2006 ident: 29_22189101 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btl158 – volume: 15 start-page: 643 issn: 1741-0126 issue: 8 year: 2002 ident: 69_17269867 publication-title: Protein Engineering Design and Selection doi: 10.1093/protein/15.8.643 – volume: 27 start-page: 3348 issn: 1367-4803 issue: 24 year: 2011 ident: 37_40952907 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr560 – volume: 19 start-page: 1309 issn: 1088-9051 issue: 7 year: 2009 ident: 58_34822443 publication-title: Genome Research doi: 10.1101/gr.089151.108 – volume: 13 start-page: 2178 issn: 1088-9051 issue: 9 year: 2003 ident: 25_17795155 publication-title: Genome Research doi: 10.1101/gr.1224503 – volume: 11 start-page: 187 issn: 1471-2105 year: 2010 ident: 13_37108173 publication-title: BMC bioinformatics [electronic resource] doi: 10.1186/1471-2105-11-187 – volume: 6 start-page: e1000667 issn: 1553-734X issue: 2 year: 2010 ident: 2_36737560 doi: 10.1371/journal.pcbi.1000667 – volume: 6 start-page: S3 issn: 1471-2105 year: 2005 ident: 36_27102599 publication-title: BMC bioinformatics [electronic resource] – volume: 12 start-page: 271 issn: 1471-2105 year: 2011 ident: 40_40258483 publication-title: BMC bioinformatics [electronic resource] doi: 10.1186/1471-2105-12-271 – volume: 12 start-page: 444 issn: 1471-2164 year: 2011 ident: 43_40734695 publication-title: BMC genomics [electronic resource] doi: 10.1186/1471-2164-12-444 – volume: 71 start-page: 1501 issn: 0099-2240 issue: 3 year: 2005 ident: 49_18715428 publication-title: Applied and Environmental Microbiology doi: 10.1128/AEM.71.3.1501-1506.2005 – volume: 35 start-page: 7188 issn: 0305-1048 issue: 21 year: 2007 ident: 70_29729501 publication-title: Nucleic Acids Research doi: 10.1093/nar/gkm864 – volume: 9 start-page: 386 issn: 1471-2105 year: 2008 ident: 45_32006915 publication-title: BMC bioinformatics [electronic resource] doi: 10.1186/1471-2105-9-386 – volume: 28 start-page: 49 issn: 0305-1048 issue: 1 year: 2000 ident: 18_6399185 publication-title: Nucleic Acids Research doi: 10.1093/nar/28.1.49 – volume: 3 start-page: e3375 issn: 1932-6203 issue: 10 year: 2008 ident: 15_32164888 doi: 10.1371/journal.pone.0003375 – volume: 12 start-page: 1889 issn: 1462-2920 issue: 7 year: 2010 ident: 52_36898660 publication-title: Environmental Microbiology (Print) doi: 10.1111/j.1462-2920.2010.02193.x – volume: 7 start-page: 668 issn: 1548-7091 issue: 9 year: 2010 ident: 55_38032744 doi: 10.1038/nmeth0910-668b – volume: 23 start-page: 1282 issn: 1367-4803 issue: 10 year: 2007 ident: 38_27960295 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btm098 – volume: 72 start-page: 5069 issn: 0099-2240 issue: 7 year: 2006 ident: 72_22337314 publication-title: Applied and Environmental Microbiology doi: 10.1128/AEM.03006-05 – volume: 9 start-page: 1135 issn: 1088-9051 issue: 11 year: 1999 ident: 34_6374359 publication-title: Genome Research doi: 10.1101/gr.9.11.1135 – volume: 27 start-page: 2502 issn: 1367-4803 issue: 18 year: 2011 ident: 41_40451192 publication-title: Bioinformatics doi: 10.1093/bioinformatics/btr447 – volume: 452 start-page: 629 issn: 1476-4687 issue: 7187 year: 2008 ident: 7_30759130 publication-title: Nature; Physical Science (London) doi: 10.1038/nature06810 – reference: 18846219 - PLoS One. 2008;3(10):e3375 – reference: 21899761 - BMC Genomics. 2011;12:444 – reference: 10871268 - Bioinformatics. 2000 May;16(5):458-64 – reference: 19819907 - Genome Res. 2009 Dec;19(12):2317-23 – reference: 21718538 - BMC Bioinformatics. 2011;12:271 – reference: 21575167 - BMC Bioinformatics. 2011;12:159 – reference: 21810899 - Bioinformatics. 2011 Sep 15;27(18):2502-9 – reference: 17355171 - PLoS Biol. 2007 Mar;5(3):e16 – reference: 15845853 - Science. 2005 Apr 22;308(5721):554-7 – reference: 20180275 - Genome Inform. 2009 Oct;23(1):205-11 – reference: 20973743 - J Comput Biol. 2010 Nov;17(11):1549-60 – reference: 20709691 - Bioinformatics. 2010 Oct 1;26(19):2460-1 – reference: 21505035 - Bioinformatics. 2011 Jun 15;27(12):1704-5 – reference: 19920124 - Nucleic Acids Res. 2010 Jan;38(Database issue):D211-22 – reference: 18402669 - BMC Bioinformatics. 2008;9:182 – reference: 18586742 - Bioinformatics. 2008 Jul 1;24(13):i41-9 – reference: 15746353 - Appl Environ Microbiol. 2005 Mar;71(3):1501-6 – reference: 20388221 - BMC Bioinformatics. 2010;11:187 – reference: 18725995 - PLoS One. 2008;3(8):e3042 – reference: 19497933 - Bioinformatics. 2009 Aug 1;25(15):1966-7 – reference: 10871267 - Bioinformatics. 2000 May;16(5):451-7 – reference: 11932250 - Genome Res. 2002 Apr;12(4):656-64 – reference: 21045053 - Nucleic Acids Res. 2011 Jan;39(Database issue):D546-51 – reference: 12651724 - Bioinformatics. 2003 Mar 22;19(5):651-2 – reference: 20236171 - Environ Microbiol. 2010 Jul;12(7):1889-98 – reference: 21276213 - BMC Bioinformatics. 2011;12:38 – reference: 17947321 - Nucleic Acids Res. 2007;35(21):7188-96 – reference: 10716175 - Protein Sci. 2000 Feb;9(2):232-41 – reference: 16026600 - BMC Bioinformatics. 2005;6 Suppl 2:S3 – reference: 15001713 - Science. 2004 Apr 2;304(5667):66-74 – reference: 20019144 - Genome Res. 2010 Feb;20(2):265-72 – reference: 19587772 - ISME J. 2009 Nov;3(11):1314-7 – reference: 19801464 - Appl Environ Microbiol. 2009 Dec;75(23):7537-41 – reference: 20195499 - PLoS Comput Biol. 2010 Feb;6(2):e1000667 – reference: 11836214 - Bioinformatics. 2002 Jan;18(1):77-82 – reference: 11294794 - Bioinformatics. 2001 Mar;17(3):282-3 – reference: 21685062 - Bioinformatics. 2011 Jul 1;27(13):i137-41 – reference: 19725865 - Environ Microbiol. 2010 Jan;12(1):118-23 – reference: 20203603 - Nature. 2010 Mar 4;464(7285):59-65 – reference: 19417062 - Nucleic Acids Res. 2009 Jun;37(10):e76 – reference: 16820507 - Appl Environ Microbiol. 2006 Jul;72(7):5069-72 – reference: 19439514 - Genome Res. 2009 Jul;19(7):1309-15 – reference: 16731699 - Bioinformatics. 2006 Jul 1;22(13):1658-9 – reference: 18337718 - Nature. 2008 Apr 3;452(7187):629-32 – reference: 12520020 - Nucleic Acids Res. 2003 Jan 1;31(1):348-52 – reference: 15590779 - Microbiol Mol Biol Rev. 2004 Dec;68(4):669-85 – reference: 18349386 - Genome Res. 2008 May;18(5):821-9 – reference: 7670480 - Nat Genet. 1995 Aug;10(4):369-71 – reference: 21273488 - Science. 2011 Jan 28;331(6016):463-7 – reference: 9847135 - Nucleic Acids Res. 1999 Jan 1;27(1):29-34 – reference: 18803844 - BMC Bioinformatics. 2008;9:386 – reference: 20383131 - Nat Methods. 2010 May;7(5):335-6 – reference: 20805793 - Nat Methods. 2010 Sep;7(9):668-9 – reference: 11917018 - Nucleic Acids Res. 2002 Apr 1;30(7):1575-84 – reference: 12364578 - Protein Eng. 2002 Aug;15(8):643-9 – reference: 19043404 - Nature. 2009 Jan 22;457(7228):480-4 – reference: 17355176 - PLoS Biol. 2007 Mar;5(3):e77 – reference: 20053844 - Bioinformatics. 2010 Mar 1;26(5):680-2 – reference: 10568753 - Genome Res. 1999 Nov;9(11):1135-42 – reference: 19892944 - Science. 2009 Dec 18;326(5960):1694-7 – reference: 19863816 - BMC Bioinformatics. 2009;10:359 – reference: 21525143 - Brief Bioinform. 2012 Jan;13(1):107-21 – reference: 17028096 - Nucleic Acids Res. 2006;34(19):5623-30 – reference: 16741115 - Science. 2006 Jun 2;312(5778):1355-9 – reference: 19004872 - Nucleic Acids Res. 2009 Jan;37(Database issue):D141-5 – reference: 10592179 - Nucleic Acids Res. 2000 Jan 1;28(1):49-55 – reference: 12824419 - Nucleic Acids Res. 2003 Jul 1;31(13):3789-91 – reference: 17379688 - Bioinformatics. 2007 May 15;23(10):1282-8 – reference: 21482625 - Genome Res. 2011 Jul;21(7):1181-92 – reference: 12386002 - Bioinformatics. 2002;18 Suppl 2:S182-91 – reference: 12952885 - Genome Res. 2003 Sep;13(9):2178-89 – reference: 21307932 - Nature. 2011 Feb 10;470(7333):198-203 – reference: 9254694 - Nucleic Acids Res. 1997 Sep 1;25(17):3389-402 – reference: 19451168 - Bioinformatics. 2009 Jul 15;25(14):1754-60 – reference: 19668203 - Nat Methods. 2009 Sep;6(9):639-41 – reference: 21984769 - Bioinformatics. 2011 Dec 15;27(24):3348-55 – reference: 12835265 - Bioinformatics. 2003 Jul 1;19(10):1221-6 – reference: 17932063 - Nucleic Acids Res. 2008 Jan;36(Database issue):D534-8 – reference: 21926975 - Nat Biotechnol. 2011 Oct;29(10):915-21
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Snippet	The rapid advances of high-throughput sequencing technologies dramatically prompted metagenomic studies of microbial communities that exist at various...
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SubjectTerms	Algorithms Bioinformatics Cluster Analysis Data analysis Errors Genomics Metagenome Metagenomics Microbial activity Microbiology Sequence Analysis, DNA
Title	Ultrafast clustering algorithms for metagenomic sequence analysis
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