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Items: 1 to 20 of 348

1.

Local alignment of two-base encoded DNA sequence.

Homer N, Merriman B, Nelson SF.

BMC Bioinformatics. 2009 Jun 9;10:175. doi: 10.1186/1471-2105-10-175.

2.

Local alignment of generalized k-base encoded DNA sequence.

Homer N, Nelson SF, Merriman B.

BMC Bioinformatics. 2010 Jun 24;11:347. doi: 10.1186/1471-2105-11-347.

3.

Fast, optimal alignment of three sequences using linear gap costs.

Powell DR, Allison L, Dix TI.

J Theor Biol. 2000 Dec 7;207(3):325-36.

PMID:
11082303
4.

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
5.

A new approach to sequence comparison: normalized sequence alignment.

Arslan AN, Eğecioğlu O, Pevzner PA.

Bioinformatics. 2001 Apr;17(4):327-37.

PMID:
11301301
6.
7.

Sequence alignment and penalty choice. Review of concepts, case studies and implications.

Vingron M, Waterman MS.

J Mol Biol. 1994 Jan 7;235(1):1-12. Review.

PMID:
8289235
8.

Clustering exact matches of pairwise sequence alignments by weighted linear regression.

González AJ, Liao L.

BMC Bioinformatics. 2008 Feb 18;9:102. doi: 10.1186/1471-2105-9-102.

9.

Segmentation of short human exons based on spectral features of double curves.

Jiang R, Yan H.

Int J Data Min Bioinform. 2008;2(1):15-35.

PMID:
18399326
10.

Local multiple alignment by consensus matrix.

Alexandrov NN.

Comput Appl Biosci. 1992 Aug;8(4):339-45.

PMID:
1498689
11.

SGA: a grammar-based alignment algorithm.

Hu G, Shen S, Ruan J.

Comput Methods Programs Biomed. 2007 Apr;86(1):17-20. Epub 2007 Jan 30.

PMID:
17267067
12.

Alignment of minisatellite maps based on run-length encoding scheme.

Abouelhoda MI, Giegerich R, Behzadi B, Steyaert JM.

J Bioinform Comput Biol. 2009 Apr;7(2):287-308.

PMID:
19340916
13.

A fractional programming approach to efficient DNA melting temperature calculation.

Leber M, Kaderali L, Schönhuth A, Schrader R.

Bioinformatics. 2005 May 15;21(10):2375-82. Epub 2005 Mar 15.

PMID:
15769839
14.

Parametric and ensemble sequence alignment algorithms.

Waterman MS.

Bull Math Biol. 1994 Jul;56(4):743-67.

PMID:
8054893
15.

Advanced computational techniques for re-sequencing DNA with polymerase signaling assay arrays.

Pe'er I, Arbili N, Liu Y, Enck C, Gelfand CA, Shamir R.

Nucleic Acids Res. 2003 Oct 1;31(19):5667-75.

16.

Database similarity searches.

Plewniak F.

Methods Mol Biol. 2008;484:361-78. doi: 10.1007/978-1-59745-398-1_24.

PMID:
18592192
17.

CUDA compatible GPU cards as efficient hardware accelerators for Smith-Waterman sequence alignment.

Manavski SA, Valle G.

BMC Bioinformatics. 2008 Mar 26;9 Suppl 2:S10. doi: 10.1186/1471-2105-9-S2-S10.

18.

A local algorithm for DNA sequence alignment with inversions.

Schöniger M, Waterman MS.

Bull Math Biol. 1992 Jul;54(4):521-36.

PMID:
1591531
19.

Alignment and prediction of cis-regulatory modules based on a probabilistic model of evolution.

He X, Ling X, Sinha S.

PLoS Comput Biol. 2009 Mar;5(3):e1000299. doi: 10.1371/journal.pcbi.1000299. Epub 2009 Mar 13.

20.

A space-efficient algorithm for local similarities.

Huang XQ, Hardison RC, Miller W.

Comput Appl Biosci. 1990 Oct;6(4):373-81.

PMID:
2257499

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