Format
Sort by
Items per page

Send to

Choose Destination

Links from PubMed

Items: 1 to 20 of 103

1.

Empirical determination of effective gap penalties for sequence comparison.

Reese JT, Pearson WR.

Bioinformatics. 2002 Nov;18(11):1500-7.

PMID:
12424122
2.

Flexible sequence similarity searching with the FASTA3 program package.

Pearson WR.

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

PMID:
10547837
3.

Pairwise statistical significance and empirical determination of effective gap opening penalties for protein local sequence alignment.

Agrawal A, Brendel VP, Huang X.

Int J Comput Biol Drug Des. 2008;1(4):347-67. Review.

PMID:
20063463
4.

Comparison of linear gap penalties and profile-based variable gap penalties in profile-profile alignments.

Wang C, Yan RX, Wang XF, Si JN, Zhang Z.

Comput Biol Chem. 2011 Oct 12;35(5):308-18. doi: 10.1016/j.compbiolchem.2011.07.006. Epub 2011 Jul 22.

PMID:
22000802
5.
6.
7.

Sequence alignment with an appropriate substitution matrix.

Huang X.

J Comput Biol. 2008 Mar;15(2):129-38. doi: 10.1089/cmb.2007.0155.

PMID:
18312146
8.

Optimizing substitution matrices by separating score distributions.

Hourai Y, Akutsu T, Akiyama Y.

Bioinformatics. 2004 Apr 12;20(6):863-73. Epub 2004 Jan 29.

PMID:
14752003
9.

Empirical and structural models for insertions and deletions in the divergent evolution of proteins.

Benner SA, Cohen MA, Gonnet GH.

J Mol Biol. 1993 Feb 20;229(4):1065-82.

PMID:
8445636
10.

A metric model of amino acid substitution.

Xu W, Miranker DP.

Bioinformatics. 2004 May 22;20(8):1214-21. Epub 2004 Feb 10. Erratum in: Bioinformatics. 2004 Dec 12;20(18):3716.

PMID:
14871874
11.
12.

Selecting the Right Similarity-Scoring Matrix.

Pearson WR.

Curr Protoc Bioinformatics. 2013;43:3.5.1-9. doi: 10.1002/0471250953.bi0305s43.

13.
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.
17.

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
18.

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.

20.

Variable gap penalty for protein sequence-structure alignment.

Madhusudhan MS, Marti-Renom MA, Sanchez R, Sali A.

Protein Eng Des Sel. 2006 Mar;19(3):129-33. Epub 2006 Jan 19.

PMID:
16423846

Supplemental Content

Support Center