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Results: 1 to 20 of 103

1.
2.

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
3.

Recent Hits Acquired by BLAST (ReHAB): a tool to identify new hits in sequence similarity searches.

Whitney J, Esteban DJ, Upton C.

BMC Bioinformatics. 2005 Feb 8;6:23.

PMID:
15701178
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments.

Gelly JC, Chiche L, Gracy J.

BMC Bioinformatics. 2005 Jan 10;6:4.

PMID:
15638949
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

fastSCOP: a fast web server for recognizing protein structural domains and SCOP superfamilies.

Tung CH, Yang JM.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W438-43. Epub 2007 May 7.

PMID:
17485476
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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
[PubMed - indexed for MEDLINE]
Free Article
7.

Protein database searches using compositionally adjusted substitution matrices.

Altschul SF, Wootton JC, Gertz EM, Agarwala R, Morgulis A, Schäffer AA, Yu YK.

FEBS J. 2005 Oct;272(20):5101-9. Review.

PMID:
16218944
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

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
[PubMed - indexed for MEDLINE]
9.

An amino acid substitution matrix for protein conformation identification.

Liu X, Zheng WM.

J Bioinform Comput Biol. 2006 Jun;4(3):769-82.

PMID:
16960974
[PubMed - indexed for MEDLINE]
10.

Protein structure database search and evolutionary classification.

Yang JM, Tung CH.

Nucleic Acids Res. 2006 Aug 2;34(13):3646-59. Print 2006.

PMID:
16885238
[PubMed - indexed for MEDLINE]
Free PMC Article
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.

QSCOP-BLAST--fast retrieval of quantified structural information for protein sequences of unknown structure.

Suhrer SJ, Gruber M, Sippl MJ.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W411-5. Epub 2007 May 3.

PMID:
17478501
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

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]
14.

FROST: a filter-based fold recognition method.

Marin A, Pothier J, Zimmermann K, Gibrat JF.

Proteins. 2002 Dec 1;49(4):493-509.

PMID:
12402359
[PubMed - indexed for MEDLINE]
15.

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
[PubMed - indexed for MEDLINE]
16.

Protein structure mining using a structural alphabet.

Tyagi M, de Brevern AG, Srinivasan N, Offmann B.

Proteins. 2008 May 1;71(2):920-37.

PMID:
18004784
[PubMed - indexed for MEDLINE]
17.

A table-driven, full-sensitivity similarity search algorithm.

Myers G, Durbin R.

J Comput Biol. 2003;10(2):103-17.

PMID:
12804086
[PubMed - indexed for MEDLINE]
18.

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
19.

Identification of new claudin family members by a novel PSI-BLAST based approach with enhanced specificity.

Wu J, Helftenbein G, Koslowski M, Sahin U, Tureci O.

Proteins. 2006 Dec 1;65(4):808-15.

PMID:
17022085
[PubMed - indexed for MEDLINE]
20.

Organizing and updating whole genome BLAST searches with ReHAB.

Esteban DJ, Syed A, Upton C.

Methods Mol Biol. 2007;395:187-94.

PMID:
17993674
[PubMed - indexed for MEDLINE]

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