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Results: 1 to 20 of 89

1.

Having a BLAST with bioinformatics (and avoiding BLASTphemy).

Pertsemlidis A, Fondon JW 3rd.

Genome Biol. 2001;2(10):REVIEWS2002. Epub 2001 Sep 27.

PMID:
11597340
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

Using BLAST for performing sequence alignment.

Healy MD.

Curr Protoc Hum Genet. 2007 Jan;Chapter 6:Unit 6.8. doi: 10.1002/0471142905.hg0608s52.

PMID:
18428415
[PubMed - indexed for MEDLINE]
3.

An I/O device driver for bioinformatics tools: the case for BLAST.

Mauro RC, Lifschitz S.

Genet Mol Res. 2005 Sep 30;4(3):563-70.

PMID:
16342041
[PubMed - indexed for MEDLINE]
4.

Improved gapped alignment in BLAST.

Cameron M, Williams HE, Cannane A.

IEEE/ACM Trans Comput Biol Bioinform. 2004 Jul-Sep;1(3):116-29.

PMID:
17048387
[PubMed - indexed for MEDLINE]
5.

Identifying remote protein homologs by network propagation.

Noble WS, Kuang R, Leslie C, Weston J.

FEBS J. 2005 Oct;272(20):5119-28. Review.

PMID:
16218946
[PubMed - indexed for MEDLINE]
Free Article
6.

GPU-BLAST: using graphics processors to accelerate protein sequence alignment.

Vouzis PD, Sahinidis NV.

Bioinformatics. 2011 Jan 15;27(2):182-8. doi: 10.1093/bioinformatics/btq644. Epub 2010 Nov 18.

PMID:
21088027
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

SS-Wrapper: a package of wrapper applications for similarity searches on Linux clusters.

Wang C, Lefkowitz EJ.

BMC Bioinformatics. 2004 Oct 28;5:171.

PMID:
15511296
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

Efficient computation of spaced seeds.

Ilie S.

BMC Res Notes. 2012 Feb 28;5:123. doi: 10.1186/1756-0500-5-123.

PMID:
22373455
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

An efficient algorithm after ungapped analysis in BLAST.

Garg D, Saxena SC, Bhardwaj LM.

DNA Seq. 2006 Aug;17(4):247-53. Retraction in: DNA Seq. 2007 Oct;18(5):405.

PMID:
17312943
[PubMed - indexed for MEDLINE]
10.

Finding homologs to nucleotide sequences using network BLAST searches.

Ladunga I.

Curr Protoc Bioinformatics. 2002 Aug;Chapter 3:Unit 3.3. doi: 10.1002/0471250953.bi0303s00. Review.

PMID:
18792938
[PubMed - indexed for MEDLINE]
11.

Finding similar nucleotide sequences using network BLAST searches.

Ladunga I.

Curr Protoc Bioinformatics. 2009 Jun;Chapter 3:Unit 3.3. doi: 10.1002/0471250953.bi0303s26.

PMID:
19496060
[PubMed - indexed for MEDLINE]
12.

Inferring function from homology.

Emes RD.

Methods Mol Biol. 2008;453:149-68. doi: 10.1007/978-1-60327-429-6_6.

PMID:
18712301
[PubMed - indexed for MEDLINE]
13.

Parallelisation of the blast algorithm.

Qi Y, Lin F.

Cell Mol Biol Lett. 2005;10(2):281-5.

PMID:
16010293
[PubMed - indexed for MEDLINE]
Free Article
14.

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. Epub 2009 Apr 10.

PMID:
19366648
[PubMed - indexed for MEDLINE]
15.

Code optimization of the subroutine to remove near identical matches in the sequence database homology search tool PSI-BLAST.

Aspnäs M, Mattila K, Osowski K, Westerholm J.

J Comput Biol. 2010 Jun;17(6):819-23. doi: 10.1089/cmb.2008.0053.

PMID:
20583927
[PubMed - indexed for MEDLINE]
16.

A novel partial sequence alignment tool for finding large deletions.

Aruk T, Ustek D, Kursun O.

ScientificWorldJournal. 2012;2012:694813. doi: 10.1100/2012/694813. Epub 2012 Apr 1.

PMID:
22566777
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

BOV--a web-based BLAST output visualization tool.

Gollapudi R, Revanna KV, Hemmerich C, Schaack S, Dong Q.

BMC Genomics. 2008 Sep 15;9:414. doi: 10.1186/1471-2164-9-414.

PMID:
18793422
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Sequence similarity searching using the BLAST family of programs.

Wolfsberg TG, Madden TL.

Curr Protoc Mol Biol. 2001 May;Chapter 19:Unit 19.3. doi: 10.1002/0471142727.mb1903s46.

PMID:
18265177
[PubMed - indexed for MEDLINE]
19.

BLAST: improvements for better sequence analysis.

Ye J, McGinnis S, Madden TL.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W6-9.

PMID:
16845079
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Installing, maintaining, and using a local copy of BLAST for intranet and workstation use.

Littlejohn TG.

Curr Protoc Bioinformatics. 2004 May;Chapter 3:Unit 3.11. doi: 10.1002/0471250953.bi0311s05.

PMID:
18428721
[PubMed - indexed for MEDLINE]

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