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Results: 1 to 20 of 98

1.

Compression of nucleotide databases for fast searching.

Williams H, Zobel J.

Comput Appl Biosci. 1997 Oct;13(5):549-54.

PMID:
9367128
[PubMed - indexed for MEDLINE]
2.

SSAHA: a fast search method for large DNA databases.

Ning Z, Cox AJ, Mullikin JC.

Genome Res. 2001 Oct;11(10):1725-9.

PMID:
11591649
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

Protein structural similarity search by Ramachandran codes.

Lo WC, Huang PJ, Chang CH, Lyu PC.

BMC Bioinformatics. 2007 Aug 23;8:307.

PMID:
17716377
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

Query-dependent banding (QDB) for faster RNA similarity searches.

Nawrocki EP, Eddy SR.

PLoS Comput Biol. 2007 Mar 30;3(3):e56. Epub 2007 Feb 7.

PMID:
17397253
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Comparing compressed sequences for faster nucleotide BLAST searches.

Cameron M, Williams HE.

IEEE/ACM Trans Comput Biol Bioinform. 2007 Jul-Sep;4(3):349-64.

PMID:
17666756
[PubMed - indexed for MEDLINE]
6.

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
7.

Fast and accurate database homology search using upper bounds of local alignment scores.

Itoh M, Goto S, Akutsu T, Kanehisa M.

Bioinformatics. 2005 Apr 1;21(7):912-21. Epub 2004 Oct 27.

PMID:
15509606
[PubMed - indexed for MEDLINE]
Free Article
8.

Serial BLAST searching.

Korf I.

Bioinformatics. 2003 Aug 12;19(12):1492-6.

PMID:
12912829
[PubMed - indexed for MEDLINE]
Free Article
9.

Issues in searching molecular sequence databases.

Altschul SF, Boguski MS, Gish W, Wootton JC.

Nat Genet. 1994 Feb;6(2):119-29. Review.

PMID:
8162065
[PubMed - indexed for MEDLINE]
10.

General-purpose search techniques for genomic text.

Chattaraj A, Williams HE, Cannane A.

Genome Inform. 2004;15(2):42-51.

PMID:
15706490
[PubMed - indexed for MEDLINE]
11.

The EMBL Nucleotide Sequence Database.

Stoesser G, Baker W, van den Broek A, Camon E, Garcia-Pastor M, Kanz C, Kulikova T, Leinonen R, Lin Q, Lombard V, Lopez R, Redaschi N, Stoehr P, Tuli MA, Tzouvara K, Vaughan R.

Nucleic Acids Res. 2002 Jan 1;30(1):21-6.

PMID:
11752244
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

Using relational databases for improved sequence similarity searching and large-scale genomic analyses.

Mackey AJ, Pearson WR.

Curr Protoc Bioinformatics. 2004 Oct;Chapter 9:Unit 9.4. doi: 10.1002/0471250953.bi0904s7.

PMID:
18428739
[PubMed - indexed for MEDLINE]
13.

Nested Containment List (NCList): a new algorithm for accelerating interval query of genome alignment and interval databases.

Alekseyenko AV, Lee CJ.

Bioinformatics. 2007 Jun 1;23(11):1386-93. Epub 2007 Jan 18.

PMID:
17234640
[PubMed - indexed for MEDLINE]
Free Article
14.

PatMaN: rapid alignment of short sequences to large databases.

Prüfer K, Stenzel U, Dannemann M, Green RE, Lachmann M, Kelso J.

Bioinformatics. 2008 Jul 1;24(13):1530-1. doi: 10.1093/bioinformatics/btn223. Epub 2008 May 8.

PMID:
18467344
[PubMed - indexed for MEDLINE]
Free PMC Article
15.

Flexible sequence similarity searching with the FASTA3 program package.

Pearson WR.

Methods Mol Biol. 2000;132:185-219.

PMID:
10547837
[PubMed - indexed for MEDLINE]
16.

The Genome Sequence DataBase: towards an integrated functional genomics resource.

Skupski MP, Booker M, Farmer A, Harpold M, Huang W, Inman J, Kiphart D, Kodira C, Root S, Schilkey F, Schwertfeger J, Siepel A, Stamper D, Thayer N, Thompson R, Wortman J, Zhuang JJ, Harger C.

Nucleic Acids Res. 1999 Jan 1;27(1):35-8.

PMID:
9847136
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

The BioPrompt-box: an ontology-based clustering tool for searching in biological databases.

Corsi C, Ferragina P, Marangoni R.

BMC Bioinformatics. 2007 Mar 8;8 Suppl 1:S8.

PMID:
17430575
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

Rapid 3D protein structure database searching using information retrieval techniques.

Aung Z, Tan KL.

Bioinformatics. 2004 May 1;20(7):1045-52. Epub 2004 Feb 12.

PMID:
14962928
[PubMed - indexed for MEDLINE]
Free Article
19.

Shape based indexing for faster search of RNA family databases.

Janssen S, Reeder J, Giegerich R.

BMC Bioinformatics. 2008 Feb 29;9:131. doi: 10.1186/1471-2105-9-131.

PMID:
18312625
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

Techniques for optimization of queries on integrated biological resources.

Lacroix Z, Raschid L, Eckman BA.

J Bioinform Comput Biol. 2004 Jun;2(2):375-411. Review.

PMID:
15297988
[PubMed - indexed for MEDLINE]

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