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Items: 1 to 20 of 95

1.

Estimation of pairwise sequence similarity of mammalian enhancers with word neighbourhood counts.

Göke J, Schulz MH, Lasserre J, Vingron M.

Bioinformatics. 2012 Mar 1;28(5):656-63. doi: 10.1093/bioinformatics/bts028. Epub 2012 Jan 12.

2.

Beyond Fixed-Resolution Alignment-Free Measures for Mammalian Enhancers Sequence Comparison.

Comin M, Verzotto D.

IEEE/ACM Trans Comput Biol Bioinform. 2014 Jul-Aug;11(4):628-37. doi: 10.1109/TCBB.2014.2306830.

PMID:
26356333
3.

On the comparison of regulatory sequences with multiple resolution Entropic Profiles.

Comin M, Antonello M.

BMC Bioinformatics. 2016 Mar 18;17:130. doi: 10.1186/s12859-016-0980-2.

4.

An alignment-free method to identify candidate orthologous enhancers in multiple Drosophila genomes.

Arunachalam M, Jayasurya K, Tomancak P, Ohler U.

Bioinformatics. 2010 Sep 1;26(17):2109-15. doi: 10.1093/bioinformatics/btq358. Epub 2010 Jul 11.

5.

Clustering protein sequences--structure prediction by transitive homology.

Bolten E, Schliep A, Schneckener S, Schomburg D, Schrader R.

Bioinformatics. 2001 Oct;17(10):935-41.

PMID:
11673238
6.

Multiple alignment-free sequence comparison.

Ren J, Song K, Sun F, Deng M, Reinert G.

Bioinformatics. 2013 Nov 1;29(21):2690-8. doi: 10.1093/bioinformatics/btt462. Epub 2013 Aug 29.

7.

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
8.

Spaced words and kmacs: fast alignment-free sequence comparison based on inexact word matches.

Horwege S, Lindner S, Boden M, Hatje K, Kollmar M, Leimeister CA, Morgenstern B.

Nucleic Acids Res. 2014 Jul;42(Web Server issue):W7-11. doi: 10.1093/nar/gku398. Epub 2014 May 14.

9.

Segment-based multiple sequence alignment.

Rausch T, Emde AK, Weese D, Döring A, Notredame C, Reinert K.

Bioinformatics. 2008 Aug 15;24(16):i187-92. doi: 10.1093/bioinformatics/btn281.

PMID:
18689823
10.

Sequence conservation and combinatorial complexity of Drosophila neural precursor cell enhancers.

Brody T, Rasband W, Baler K, Kuzin A, Kundu M, Odenwald WF.

BMC Genomics. 2008 Aug 1;9:371. doi: 10.1186/1471-2164-9-371.

11.

An alignment-free model for comparison of regulatory sequences.

Koohy H, Dyer NP, Reid JE, Koentges G, Ott S.

Bioinformatics. 2010 Oct 1;26(19):2391-7. doi: 10.1093/bioinformatics/btq453. Epub 2010 Aug 9.

PMID:
20696736
12.

A statistical method for alignment-free comparison of regulatory sequences.

Kantorovitz MR, Robinson GE, Sinha S.

Bioinformatics. 2007 Jul 1;23(13):i249-55.

PMID:
17646303
13.

GeneHancer: genome-wide integration of enhancers and target genes in GeneCards.

Fishilevich S, Nudel R, Rappaport N, Hadar R, Plaschkes I, Iny Stein T, Rosen N, Kohn A, Twik M, Safran M, Lancet D, Cohen D.

Database (Oxford). 2017 Jan 1;2017. doi: 10.1093/database/bax028.

14.

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
15.

MicroRazerS: rapid alignment of small RNA reads.

Emde AK, Grunert M, Weese D, Reinert K, Sperling SR.

Bioinformatics. 2010 Jan 1;26(1):123-4. doi: 10.1093/bioinformatics/btp601. Epub 2009 Oct 29.

PMID:
19880369
16.

Integrating alignment-based and alignment-free sequence similarity measures for biological sequence classification.

Borozan I, Watt S, Ferretti V.

Bioinformatics. 2015 May 1;31(9):1396-404. doi: 10.1093/bioinformatics/btv006. Epub 2015 Jan 7.

17.

Discriminative prediction of mammalian enhancers from DNA sequence.

Lee D, Karchin R, Beer MA.

Genome Res. 2011 Dec;21(12):2167-80. doi: 10.1101/gr.121905.111. Epub 2011 Aug 29.

18.

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.

19.

Twine: display and analysis of cis-regulatory modules.

Pearson JC, Crews ST.

Bioinformatics. 2013 Jul 1;29(13):1690-2. doi: 10.1093/bioinformatics/btt264. Epub 2013 May 8.

20.

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.

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