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Items: 1 to 20 of 87

1.

BRM-Parser: a tool for comprehensive analysis of BLAST and RepeatMasker results.

Bajpai A, Sridhar S, Reddy HM, Jesudasan RA.

In Silico Biol. 2007;7(4-5):399-403.

PMID:
18391232
2.

Windows .NET Network Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST).

Dowd SE, Zaragoza J, Rodriguez JR, Oliver MJ, Payton PR.

BMC Bioinformatics. 2005 Apr 8;6:93.

3.

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.

4.

Transposable element annotation of the rice genome.

Juretic N, Bureau TE, Bruskiewich RM.

Bioinformatics. 2004 Jan 22;20(2):155-60.

PMID:
14734305
5.

WindowMasker: window-based masker for sequenced genomes.

Morgulis A, Gertz EM, Schäffer AA, Agarwala R.

Bioinformatics. 2006 Jan 15;22(2):134-41. Epub 2005 Nov 15.

PMID:
16287941
6.

BLAST+: architecture and applications.

Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL.

BMC Bioinformatics. 2009 Dec 15;10:421. doi: 10.1186/1471-2105-10-421.

7.

PSIBLAST_PairwiseStatSig: reordering PSI-BLAST hits using pairwise statistical significance.

Agrawal A, Huang X.

Bioinformatics. 2009 Apr 15;25(8):1082-3. doi: 10.1093/bioinformatics/btp089. Epub 2009 Feb 27.

PMID:
19251771
8.

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
9.

Using RepeatMasker to identify repetitive elements in genomic sequences.

Chen N.

Curr Protoc Bioinformatics. 2004 May;Chapter 4:Unit 4.10. doi: 10.1002/0471250953.bi0410s05.

PMID:
18428725
10.

NOBLAST and JAMBLAST: New Options for BLAST and a Java Application Manager for BLAST results.

Lagnel J, Tsigenopoulos CS, Iliopoulos I.

Bioinformatics. 2009 Mar 15;25(6):824-6. doi: 10.1093/bioinformatics/btp067. Epub 2009 Jan 29.

PMID:
19181685
11.

Distant homology detection using a LEngth and STructure-based sequence Alignment Tool (LESTAT).

Lee MM, Bundschuh R, Chan MK.

Proteins. 2008 May 15;71(3):1409-19.

PMID:
18076050
12.

Mastering seeds for genomic size nucleotide BLAST searches.

Gotea V, Veeramachaneni V, Makałowski W.

Nucleic Acids Res. 2003 Dec 1;31(23):6935-41.

13.

Using RepeatMasker to identify repetitive elements in genomic sequences.

Tarailo-Graovac M, Chen N.

Curr Protoc Bioinformatics. 2009 Mar;Chapter 4:Unit 4.10. doi: 10.1002/0471250953.bi0410s25.

PMID:
19274634
14.

Batch Blast Extractor: an automated blastx parser application.

Pirooznia M, Perkins EJ, Deng Y.

BMC Genomics. 2008 Sep 16;9 Suppl 2:S10. doi: 10.1186/1471-2164-9-S2-S10.

15.

SWeBLAST: a Sliding Window Web-based BLAST tool for recombinant analysis.

Fourment M, Gibbs AJ, Gibbs MJ.

J Virol Methods. 2008 Sep;152(1-2):98-101. doi: 10.1016/j.jviromet.2008.06.009. Epub 2008 Jul 17.

PMID:
18602951
16.
17.

Saturated BLAST: an automated multiple intermediate sequence search used to detect distant homology.

Li W, Pio F, Pawłowski K, Godzik A.

Bioinformatics. 2000 Dec;16(12):1105-10.

PMID:
11159329
18.

SIB-BLAST: a web server for improved delineation of true and false positives in PSI-BLAST searches.

Lee MM, Chan MK, Bundschuh R.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W53-6. doi: 10.1093/nar/gkp301. Epub 2009 May 8.

19.

Sequence similarity searching using the BLAST family of programs.

Wolfsberg TG, Madden TL.

Curr Protoc Protein Sci. 2001 May;Chapter 2:Unit2.5. doi: 10.1002/0471140864.ps0205s15.

PMID:
18429153
20.

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

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