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Items: 1 to 20 of 130

1.

CD-HIT: accelerated for clustering the next-generation sequencing data.

Fu L, Niu B, Zhu Z, Wu S, Li W.

Bioinformatics. 2012 Dec 1;28(23):3150-2. doi: 10.1093/bioinformatics/bts565. Epub 2012 Oct 11.

2.

Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences.

Li W, Godzik A.

Bioinformatics. 2006 Jul 1;22(13):1658-9. Epub 2006 May 26.

PMID:
16731699
3.

CD-HIT Suite: a web server for clustering and comparing biological sequences.

Huang Y, Niu B, Gao Y, Fu L, Li W.

Bioinformatics. 2010 Mar 1;26(5):680-2. doi: 10.1093/bioinformatics/btq003. Epub 2010 Jan 6.

4.

Acceleration of sequence clustering using longest common subsequence filtering.

Namiki Y, Ishida T, Akiyama Y.

BMC Bioinformatics. 2013;14 Suppl 8:S7. doi: 10.1186/1471-2105-14-S8-S7. Epub 2013 May 9.

5.

MMseqs software suite for fast and deep clustering and searching of large protein sequence sets.

Hauser M, Steinegger M, Söding J.

Bioinformatics. 2016 May 1;32(9):1323-30. doi: 10.1093/bioinformatics/btw006. Epub 2016 Jan 6.

PMID:
26743509
6.

A modified hyperplane clustering algorithm allows for efficient and accurate clustering of extremely large datasets.

Sharma A, Podolsky R, Zhao J, McIndoe RA.

Bioinformatics. 2009 May 1;25(9):1152-7. doi: 10.1093/bioinformatics/btp123. Epub 2009 Mar 4.

7.

SEED: efficient clustering of next-generation sequences.

Bao E, Jiang T, Kaloshian I, Girke T.

Bioinformatics. 2011 Sep 15;27(18):2502-9. doi: 10.1093/bioinformatics/btr447. Epub 2011 Aug 2.

8.

Application of learning to rank to protein remote homology detection.

Liu B, Chen J, Wang X.

Bioinformatics. 2015 Nov 1;31(21):3492-8. doi: 10.1093/bioinformatics/btv413. Epub 2015 Jul 10.

PMID:
26163693
9.

KABOOM! A new suffix array based algorithm for clustering expression data.

Hazelhurst S, Lipták Z.

Bioinformatics. 2011 Dec 15;27(24):3348-55. doi: 10.1093/bioinformatics/btr560. Epub 2011 Oct 8.

PMID:
21984769
10.

Probing metagenomics by rapid cluster analysis of very large datasets.

Li W, Wooley JC, Godzik A.

PLoS One. 2008;3(10):e3375. doi: 10.1371/journal.pone.0003375. Epub 2008 Oct 10.

11.

Phylogenomic analysis of bacterial and archaeal sequences with AMPHORA2.

Wu M, Scott AJ.

Bioinformatics. 2012 Apr 1;28(7):1033-4. doi: 10.1093/bioinformatics/bts079. Epub 2012 Feb 12.

PMID:
22332237
12.

Efficient functional clustering of protein sequences using the Dirichlet process.

Brown DP.

Bioinformatics. 2008 Aug 15;24(16):1765-71. doi: 10.1093/bioinformatics/btn244. Epub 2008 May 29.

PMID:
18511467
13.

APCluster: an R package for affinity propagation clustering.

Bodenhofer U, Kothmeier A, Hochreiter S.

Bioinformatics. 2011 Sep 1;27(17):2463-4. doi: 10.1093/bioinformatics/btr406. Epub 2011 Jul 6.

PMID:
21737437
14.

ArchTEx: accurate extraction and visualization of next-generation sequence data.

Lai WK, Bard JE, Buck MJ.

Bioinformatics. 2012 Apr 1;28(7):1021-3. doi: 10.1093/bioinformatics/bts063. Epub 2012 Feb 2.

PMID:
22302569
15.

QuRe: software for viral quasispecies reconstruction from next-generation sequencing data.

Prosperi MC, Salemi M.

Bioinformatics. 2012 Jan 1;28(1):132-3. doi: 10.1093/bioinformatics/btr627. Epub 2011 Nov 15.

16.

A mathematical and computational framework for quantitative comparison and integration of large-scale gene expression data.

Hart CE, Sharenbroich L, Bornstein BJ, Trout D, King B, Mjolsness E, Wold BJ.

Nucleic Acids Res. 2005 May 10;33(8):2580-94. Print 2005.

17.

A data parallel strategy for aligning multiple biological sequences on multi-core computers.

Zhu X, Li K, Salah A.

Comput Biol Med. 2013 May;43(4):350-61. doi: 10.1016/j.compbiomed.2012.12.009. Epub 2013 Feb 14.

PMID:
23414778
18.

A novel approach for clustering proteomics data using Bayesian fast Fourier transform.

Bensmail H, Golek J, Moody MM, Semmes JO, Haoudi A.

Bioinformatics. 2005 May 15;21(10):2210-24. Epub 2005 Mar 15.

PMID:
15769836
19.

A biclustering algorithm for extracting bit-patterns from binary datasets.

Rodriguez-Baena DS, Perez-Pulido AJ, Aguilar-Ruiz JS.

Bioinformatics. 2011 Oct 1;27(19):2738-45. doi: 10.1093/bioinformatics/btr464. Epub 2011 Aug 8.

PMID:
21824973
20.

Identifying and removing artificial replicates from 454 pyrosequencing data.

Teal TK, Schmidt TM.

Cold Spring Harb Protoc. 2010 Apr;2010(4):pdb.prot5409. doi: 10.1101/pdb.prot5409.

PMID:
20360363

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