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Items: 1 to 20 of 113

1.

Ultra-fast sequence clustering from similarity networks with SiLiX.

Miele V, Penel S, Duret L.

BMC Bioinformatics. 2011 Apr 22;12:116. doi: 10.1186/1471-2105-12-116.

2.

High-quality sequence clustering guided by network topology and multiple alignment likelihood.

Miele V, Penel S, Daubin V, Picard F, Kahn D, Duret L.

Bioinformatics. 2012 Apr 15;28(8):1078-85. doi: 10.1093/bioinformatics/bts098. Epub 2012 Feb 25.

PMID:
22368255
3.

CLUSS: clustering of protein sequences based on a new similarity measure.

Kelil A, Wang S, Brzezinski R, Fleury A.

BMC Bioinformatics. 2007 Aug 4;8:286.

4.

Databases of homologous gene families for comparative genomics.

Penel S, Arigon AM, Dufayard JF, Sertier AS, Daubin V, Duret L, Gouy M, Perrière G.

BMC Bioinformatics. 2009 Jun 16;10 Suppl 6:S3. doi: 10.1186/1471-2105-10-S6-S3.

5.

ProClust: improved clustering of protein sequences with an extended graph-based approach.

Pipenbacher P, Schliep A, Schneckener S, Schönhuth A, Schomburg D, Schrader R.

Bioinformatics. 2002;18 Suppl 2:S182-91.

PMID:
12386002
6.

HoSeqI: automated homologous sequence identification in gene family databases.

Arigon AM, Perrière G, Gouy M.

Bioinformatics. 2006 Jul 15;22(14):1786-7. Epub 2006 May 8.

PMID:
16682422
7.

Large scale clustering of protein sequences with FORCE -A layout based heuristic for weighted cluster editing.

Wittkop T, Baumbach J, Lobo FP, Rahmann S.

BMC Bioinformatics. 2007 Oct 17;8:396.

8.

Improving the specificity of high-throughput ortholog prediction.

Fulton DL, Li YY, Laird MR, Horsman BG, Roche FM, Brinkman FS.

BMC Bioinformatics. 2006 May 28;7:270.

9.

On the quality of tree-based protein classification.

Lazareva-Ulitsky B, Diemer K, Thomas PD.

Bioinformatics. 2005 May 1;21(9):1876-90. Epub 2005 Jan 12.

PMID:
15647305
11.

Efficient filtering methods for clustering cDNAs with spliced sequence alignment.

Shibuya T, Kashima H, Konagaya A.

Bioinformatics. 2004 Jan 1;20(1):29-39.

PMID:
14693805
12.

CLAGen: a tool for clustering and annotating gene sequences using a suffix tree algorithm.

Han Si, Lee SG, Kim KH, Choi CJ, Kim YH, Hwang KS.

Biosystems. 2006 Jun;84(3):175-82. Epub 2005 Dec 27.

PMID:
16384634
13.

TIGR Gene Indices clustering tools (TGICL): a software system for fast clustering of large EST datasets.

Pertea G, Huang X, Liang F, Antonescu V, Sultana R, Karamycheva S, Lee Y, White J, Cheung F, Parvizi B, Tsai J, Quackenbush J.

Bioinformatics. 2003 Mar 22;19(5):651-2.

PMID:
12651724
14.

NcDNAlign: plausible multiple alignments of non-protein-coding genomic sequences.

Rose D, Hertel J, Reiche K, Stadler PF, Hackermüller J.

Genomics. 2008 Jul;92(1):65-74. doi: 10.1016/j.ygeno.2008.04.003. Epub 2008 Jun 3.

15.

MATLIGN: a motif clustering, comparison and matching tool.

Kankainen M, Löytynoja A.

BMC Bioinformatics. 2007 Jun 8;8:189.

16.

AutoGRAPH: an interactive web server for automating and visualizing comparative genome maps.

Derrien T, André C, Galibert F, Hitte C.

Bioinformatics. 2007 Feb 15;23(4):498-9. Epub 2006 Dec 4.

PMID:
17145741
17.

PatMaN: rapid alignment of short sequences to large databases.

Prüfer K, Stenzel U, Dannemann M, Green RE, Lachmann M, Kelso J.

Bioinformatics. 2008 Jul 1;24(13):1530-1. doi: 10.1093/bioinformatics/btn223. Epub 2008 May 8.

18.
19.

Gene structure prediction from consensus spliced alignment of multiple ESTs matching the same genomic locus.

Brendel V, Xing L, Zhu W.

Bioinformatics. 2004 May 1;20(7):1157-69. Epub 2004 Feb 5.

PMID:
14764557
20.

RBR: library-less repeat detection for ESTs.

Malde K, Schneeberger K, Coward E, Jonassen I.

Bioinformatics. 2006 Sep 15;22(18):2232-6. Epub 2006 Jul 12.

PMID:
16837527

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