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Items: 1 to 20 of 61

1.

SWPS3 - fast multi-threaded vectorized Smith-Waterman for IBM Cell/B.E. and x86/SSE2.

Szalkowski A, Ledergerber C, Krähenbühl P, Dessimoz C.

BMC Res Notes. 2008 Oct 29;1:107. doi: 10.1186/1756-0500-1-107.

2.

Multi-threaded vectorized distance matrix computation on the CELL/BE and x86/SSE2 architectures.

Wirawan A, Kwoh CK, Schmidt B.

Bioinformatics. 2010 May 15;26(10):1368-9. doi: 10.1093/bioinformatics/btq135.

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CUDASW++: optimizing Smith-Waterman sequence database searches for CUDA-enabled graphics processing units.

Liu Y, Maskell DL, Schmidt B.

BMC Res Notes. 2009 May 6;2:73. doi: 10.1186/1756-0500-2-73.

6.

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.

7.

CellMC--a multiplatform model compiler for the Cell Broadband Engine and x86.

Caulfield E, Hellander A.

Bioinformatics. 2010 Feb 1;26(3):426-8. doi: 10.1093/bioinformatics/btp662.

8.

A new approach to sequence comparison: normalized sequence alignment.

Arslan AN, Eğecioğlu O, Pevzner PA.

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

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CBESW: sequence alignment on the Playstation 3.

Wirawan A, Kwoh CK, Hieu NT, Schmidt B.

BMC Bioinformatics. 2008 Sep 17;9:377. doi: 10.1186/1471-2105-9-377.

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A parallel pairwise local sequence alignment algorithm.

Bandyopadhyay S, Mitra R.

IEEE Trans Nanobioscience. 2009 Jun;8(2):139-46. doi: 10.1109/TNB.2009.2019642.

PMID:
19366648
14.

From analysis of protein structural alignments toward a novel approach to align protein sequences.

Sunyaev SR, Bogopolsky GA, Oleynikova NV, Vlasov PK, Finkelstein AV, Roytberg MA.

Proteins. 2004 Feb 15;54(3):569-82.

PMID:
14748004
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16.

[Comparative analysis of primary structure of nucleic acids and proteins].

Roĭtberg MA.

Mol Biol (Mosk). 2004 Jan-Feb;38(1):92-103. Review. Russian.

PMID:
15042839
17.

Sensitivity and selectivity in protein similarity searches: a comparison of Smith-Waterman in hardware to BLAST and FASTA.

Shpaer EG, Robinson M, Yee D, Candlin JD, Mines R, Hunkapiller T.

Genomics. 1996 Dec 1;38(2):179-91.

PMID:
8954800
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PatternHunter II: highly sensitive and fast homology search.

Li M, Ma B, Kisman D, Tromp J.

Genome Inform. 2003;14:164-75.

PMID:
15706531
20.

A novel Markov pairwise protein sequence alignment method for sequence comparison.

Zhao XM, Cheung YM, Huang DS.

Protein Pept Lett. 2005 Oct;12(7):665-9.

PMID:
16522182
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