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Items: 1 to 20 of 102

1.

New finite-size correction for local alignment score distributions.

Park Y, Sheetlin S, Ma N, Madden TL, Spouge JL.

BMC Res Notes. 2012 Jun 12;5:286. doi: 10.1186/1756-0500-5-286.

2.

The correlation error and finite-size correction in an ungapped sequence alignment.

Park Y, Spouge JL.

Bioinformatics. 2002 Sep;18(9):1236-42.

PMID:
12217915
3.

BLAST: improvements for better sequence analysis.

Ye J, McGinnis S, Madden TL.

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

4.

Domain enhanced lookup time accelerated BLAST.

Boratyn GM, Schäffer AA, Agarwala R, Altschul SF, Lipman DJ, Madden TL.

Biol Direct. 2012 Apr 17;7:12. doi: 10.1186/1745-6150-7-12.

5.

Genomic BLAST: custom-defined virtual databases for complete and unfinished genomes.

Cummings L, Riley L, Black L, Souvorov A, Resenchuk S, Dondoshansky I, Tatusova T.

FEMS Microbiol Lett. 2002 Nov 5;216(2):133-8.

6.

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.

7.

Searching for evolutionary distant RNA homologs within genomic sequences using partition function posterior probabilities.

Roshan U, Chikkagoudar S, Livesay DR.

BMC Bioinformatics. 2008 Jan 28;9:61. doi: 10.1186/1471-2105-9-61.

8.

BLAST: a more efficient report with usability improvements.

Boratyn GM, Camacho C, Cooper PS, Coulouris G, Fong A, Ma N, Madden TL, Matten WT, McGinnis SD, Merezhuk Y, Raytselis Y, Sayers EW, Tao T, Ye J, Zaretskaya I.

Nucleic Acids Res. 2013 Jul;41(Web Server issue):W29-33. doi: 10.1093/nar/gkt282. Epub 2013 Apr 22.

9.

Estimation of P-values for global alignments of protein sequences.

Webber C, Barton GJ.

Bioinformatics. 2001 Dec;17(12):1158-67.

PMID:
11751224
10.

OXBench: a benchmark for evaluation of protein multiple sequence alignment accuracy.

Raghava GP, Searle SM, Audley PC, Barber JD, Barton GJ.

BMC Bioinformatics. 2003 Oct 10;4:47.

11.

Finding homologs in amino acid sequences using network BLAST searches.

Ladunga I.

Curr Protoc Bioinformatics. 2003 Feb;Chapter 3:Unit 3.4. doi: 10.1002/0471250953.bi0304s00.

PMID:
18428697
12.

NCBI BLAST: a better web interface.

Johnson M, Zaretskaya I, Raytselis Y, Merezhuk Y, McGinnis S, Madden TL.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W5-9. doi: 10.1093/nar/gkn201. Epub 2008 Apr 24.

13.

Soap-HT-BLAST: high throughput BLAST based on Web services.

Wang J, Mu Q.

Bioinformatics. 2003 Sep 22;19(14):1863-4.

PMID:
14512365
14.

BLAST and FASTA similarity searching for multiple sequence alignment.

Pearson WR.

Methods Mol Biol. 2014;1079:75-101. doi: 10.1007/978-1-62703-646-7_5.

PMID:
24170396
15.

BLAST QuickStart: example-driven web-based BLAST tutorial.

Wheeler D, Bhagwat M.

Methods Mol Biol. 2007;395:149-76.

16.

ProClust: improved clustering of protein sequences with an extended graph-based approach.

Pipenbacher P, Schliep A, Schneckener S, Schönhuth A, Schomburg D, Schrader R.

Bioinformatics. 2002;18 Suppl 2:S182-91.

PMID:
12386002
17.

Clustered sequence representation for fast homology search.

Cameron M, Bernstein Y, Williams HE.

J Comput Biol. 2007 Jun;14(5):594-614. Review.

PMID:
17683263
18.

On the significance of sequence alignments when using multiple scoring matrices.

Frommlet F, Futschik A, Bogdan M.

Bioinformatics. 2004 Apr 12;20(6):881-7. Epub 2004 Jan 29.

PMID:
14751984
19.

Correcting BLAST e-values for low-complexity segments.

Sharon I, Birkland A, Chang K, El-Yaniv R, Yona G.

J Comput Biol. 2005 Sep;12(7):980-1003.

PMID:
16201917
20.

Improved BLAST searches using longer words for protein seeding.

Shiryev SA, Papadopoulos JS, Schäffer AA, Agarwala R.

Bioinformatics. 2007 Nov 1;23(21):2949-51. Epub 2007 Oct 6.

PMID:
17921491

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