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Items: 1 to 20 of 129

1.

STELLAR: fast and exact local alignments.

Kehr B, Weese D, Reinert K.

BMC Bioinformatics. 2011 Oct 5;12 Suppl 9:S15. doi: 10.1186/1471-2105-12-S9-S15.

2.

Fast and accurate read mapping with approximate seeds and multiple backtracking.

Siragusa E, Weese D, Reinert K.

Nucleic Acids Res. 2013 Apr;41(7):e78. doi: 10.1093/nar/gkt005. Epub 2013 Jan 28.

3.

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
4.

BatMis: a fast algorithm for k-mismatch mapping.

Tennakoon C, Purbojati RW, Sung WK.

Bioinformatics. 2012 Aug 15;28(16):2122-8. doi: 10.1093/bioinformatics/bts339. Epub 2012 Jun 10.

PMID:
22689389
5.

Bridges: a tool for identifying local similarities in long sequences.

Kondrashov AS, Assis R.

Bioinformatics. 2010 Aug 15;26(16):2055-6. doi: 10.1093/bioinformatics/btq320. Epub 2010 Jun 20.

PMID:
20562450
6.

Simultaneous identification of long similar substrings in large sets of sequences.

Kleffe J, Möller F, Wittig B.

BMC Bioinformatics. 2007 May 24;8 Suppl 5:S7.

7.

A min-cut algorithm for the consistency problem in multiple sequence alignment.

Corel E, Pitschi F, Morgenstern B.

Bioinformatics. 2010 Apr 15;26(8):1015-21. doi: 10.1093/bioinformatics/btq082. Epub 2010 Feb 25.

PMID:
20189940
8.

GASSST: global alignment short sequence search tool.

Rizk G, Lavenier D.

Bioinformatics. 2010 Oct 15;26(20):2534-40. doi: 10.1093/bioinformatics/btq485. Epub 2010 Aug 24.

9.

YASS: enhancing the sensitivity of DNA similarity search.

Noé L, Kucherov G.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W540-3.

10.

Long read alignment based on maximal exact match seeds.

Liu Y, Schmidt B.

Bioinformatics. 2012 Sep 15;28(18):i318-i324. doi: 10.1093/bioinformatics/bts414.

11.

Multiple alignment of genomic sequences using CHAOS, DIALIGN and ABC.

Pöhler D, Werner N, Steinkamp R, Morgenstern B.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W532-4.

12.

The CHAOS/DIALIGN WWW server for multiple alignment of genomic sequences.

Brudno M, Steinkamp R, Morgenstern B.

Nucleic Acids Res. 2004 Jul 1;32(Web Server issue):W41-4.

13.

Computing posterior probabilities for score-based alignments using ppALIGN.

Wolfsheimer S, Hartmann A, Rabus R, Nuel G.

Stat Appl Genet Mol Biol. 2012 May 16;11(4):Article 1. doi: 10.1515/1544-6115.1702.

PMID:
22628350
14.

Benchmarking tools for the alignment of functional noncoding DNA.

Pollard DA, Bergman CM, Stoye J, Celniker SE, Eisen MB.

BMC Bioinformatics. 2004 Jan 21;5:6.

15.

Compressed indexing and local alignment of DNA.

Lam TW, Sung WK, Tam SL, Wong CK, Yiu SM.

Bioinformatics. 2008 Mar 15;24(6):791-7. doi: 10.1093/bioinformatics/btn032. Epub 2008 Jan 28.

PMID:
18227115
16.

Efficient estimation of pairwise distances between genomes.

Domazet-Loso M, Haubold B.

Bioinformatics. 2009 Dec 15;25(24):3221-7. doi: 10.1093/bioinformatics/btp590. Epub 2009 Oct 13.

PMID:
19825795
17.

SCARNA: fast and accurate structural alignment of RNA sequences by matching fixed-length stem fragments.

Tabei Y, Tsuda K, Kin T, Asai K.

Bioinformatics. 2006 Jul 15;22(14):1723-9. Epub 2006 May 11.

PMID:
16690634
18.

Parasail: SIMD C library for global, semi-global, and local pairwise sequence alignments.

Daily J.

BMC Bioinformatics. 2016 Feb 10;17:81. doi: 10.1186/s12859-016-0930-z.

19.

Mulan: multiple-sequence local alignment and visualization for studying function and evolution.

Ovcharenko I, Loots GG, Giardine BM, Hou M, Ma J, Hardison RC, Stubbs L, Miller W.

Genome Res. 2005 Jan;15(1):184-94. Epub 2004 Dec 8.

20.

BLAST 2 Sequences, a new tool for comparing protein and nucleotide sequences.

Tatusova TA, Madden TL.

FEMS Microbiol Lett. 1999 May 15;174(2):247-50. Erratum in: FEMS Microbiol Lett 1999 Aug 1;177(1):187-8.

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