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Items: 1 to 50 of 86

1.

Using SQL Databases for Sequence Similarity Searching and Analysis.

Pearson WR, Mackey AJ.

Curr Protoc Bioinformatics. 2017 Sep 13;59:9.4.1-9.4.22. doi: 10.1002/cpbi.32.

PMID:
28902397
2.

Query-seeded iterative sequence similarity searching improves selectivity 5-20-fold.

Pearson WR, Li W, Lopez R.

Nucleic Acids Res. 2017 Apr 20;45(7):e46. doi: 10.1093/nar/gkw1207.

3.

Finding Protein and Nucleotide Similarities with FASTA.

Pearson WR.

Curr Protoc Bioinformatics. 2016 Mar 24;53:3.9.1-25. doi: 10.1002/0471250953.bi0309s53.

4.

Protein Function Prediction: Problems and Pitfalls.

Pearson WR.

Curr Protoc Bioinformatics. 2015 Sep 3;51:4.12.1-8. doi: 10.1002/0471250953.bi0412s51. Review.

PMID:
26334923
5.

Most partial domains in proteins are alignment and annotation artifacts.

Triant DA, Pearson WR.

Genome Biol. 2015 May 15;16:99. doi: 10.1186/s13059-015-0656-7.

6.

Selecting the Right Similarity-Scoring Matrix.

Pearson WR.

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

7.

The Catalytic Site Atlas 2.0: cataloging catalytic sites and residues identified in enzymes.

Furnham N, Holliday GL, de Beer TA, Jacobsen JO, Pearson WR, Thornton JM.

Nucleic Acids Res. 2014 Jan;42(Database issue):D485-9. doi: 10.1093/nar/gkt1243. Epub 2013 Dec 6.

8.

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
9.

Adjusting scoring matrices to correct overextended alignments.

Mills LJ, Pearson WR.

Bioinformatics. 2013 Dec 1;29(23):3007-13. doi: 10.1093/bioinformatics/btt517. Epub 2013 Aug 31.

10.

An introduction to sequence similarity ("homology") searching.

Pearson WR.

Curr Protoc Bioinformatics. 2013 Jun;Chapter 3:Unit3.1. doi: 10.1002/0471250953.bi0301s42. Review.

11.

PSI-Search: iterative HOE-reduced profile SSEARCH searching.

Li W, McWilliam H, Goujon M, Cowley A, Lopez R, Pearson WR.

Bioinformatics. 2012 Jun 15;28(12):1650-1. doi: 10.1093/bioinformatics/bts240. Epub 2012 Apr 25.

12.

MACiE: exploring the diversity of biochemical reactions.

Holliday GL, Andreini C, Fischer JD, Rahman SA, Almonacid DE, Williams ST, Pearson WR.

Nucleic Acids Res. 2012 Jan;40(Database issue):D783-9. doi: 10.1093/nar/gkr799. Epub 2011 Nov 3.

13.

RefProtDom: a protein database with improved domain boundaries and homology relationships.

Gonzalez MW, Pearson WR.

Bioinformatics. 2010 Sep 15;26(18):2361-2. doi: 10.1093/bioinformatics/btq426. Epub 2010 Aug 6.

14.

Improving pairwise sequence alignment accuracy using near-optimal protein sequence alignments.

Sierk ML, Smoot ME, Bass EJ, Pearson WR.

BMC Bioinformatics. 2010 Mar 22;11:146. doi: 10.1186/1471-2105-11-146.

15.

Homologous over-extension: a challenge for iterative similarity searches.

Gonzalez MW, Pearson WR.

Nucleic Acids Res. 2010 Apr;38(7):2177-89. doi: 10.1093/nar/gkp1219. Epub 2010 Jan 11.

16.

Globally, unrelated protein sequences appear random.

Lavelle DT, Pearson WR.

Bioinformatics. 2010 Feb 1;26(3):310-8. doi: 10.1093/bioinformatics/btp660. Epub 2009 Nov 30.

17.

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
18.

Phylogenies of glutathione transferase families.

Pearson WR.

Methods Enzymol. 2005;401:186-204. Review.

PMID:
16399387
19.

Nomenclature for mammalian soluble glutathione transferases.

Mannervik B, Board PG, Hayes JD, Listowsky I, Pearson WR.

Methods Enzymol. 2005;401:1-8.

PMID:
16399376
20.

The limits of protein sequence comparison?

Pearson WR, Sierk ML.

Curr Opin Struct Biol. 2005 Jun;15(3):254-60. Review.

21.

The genome of Cryptosporidium hominis.

Xu P, Widmer G, Wang Y, Ozaki LS, Alves JM, Serrano MG, Puiu D, Manque P, Akiyoshi D, Mackey AJ, Pearson WR, Dear PH, Bankier AT, Peterson DL, Abrahamsen MS, Kapur V, Tzipori S, Buck GA.

Nature. 2004 Oct 28;431(7012):1107-12. Erratum in: Nature. 2004 Nov 18;432(7015):415.

PMID:
15510150
22.

Sensitivity and selectivity in protein structure comparison.

Sierk ML, Pearson WR.

Protein Sci. 2004 Mar;13(3):773-85.

23.

Visualization of near-optimal sequence alignments.

Smoot ME, Guerlain SA, Pearson WR.

Bioinformatics. 2004 Apr 12;20(6):953-8. Epub 2004 Jan 29.

24.

CRP: Cleavage of Radiolabeled Phosphoproteins.

Mackey AJ, Haystead TA, Pearson WR.

Nucleic Acids Res. 2003 Jul 1;31(13):3859-61.

25.

Identification of residues in glutathione transferase capable of driving functional diversification in evolution. A novel approach to protein redesign.

Ivarsson Y, Mackey AJ, Edalat M, Pearson WR, Mannervik B.

J Biol Chem. 2003 Mar 7;278(10):8733-8. Epub 2002 Dec 16.

26.

Entamoeba histolytica: sequence conservation of the Gal/GalNAc lectin from clinical isolates.

Beck DL, Tanyuksel M, Mackey AJ, Haque R, Trapaidze N, Pearson WR, Loftus B, Petri WA.

Exp Parasitol. 2002 Jun-Jul;101(2-3):157-63.

PMID:
12427470
27.

Empirical determination of effective gap penalties for sequence comparison.

Reese JT, Pearson WR.

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

PMID:
12424122
28.

Getting more from less: algorithms for rapid protein identification with multiple short peptide sequences.

Mackey AJ, Haystead TA, Pearson WR.

Mol Cell Proteomics. 2002 Feb;1(2):139-47.

29.

A strategy for the rapid identification of phosphorylation sites in the phosphoproteome.

MacDonald JA, Mackey AJ, Pearson WR, Haystead TA.

Mol Cell Proteomics. 2002 Apr;1(4):314-22.

30.

Identification and characterization of GSTT3, a third murine Theta class glutathione transferase.

Coggan M, Flanagan JU, Parker MW, Vichai V, Pearson WR, Board PG.

Biochem J. 2002 Aug 15;366(Pt 1):323-32.

31.

Training for bioinformatics and computational biology.

Pearson WR.

Bioinformatics. 2001 Sep;17(9):761-2. No abstract available.

PMID:
11590093
32.

Flexible sequence similarity searching with the FASTA3 program package.

Pearson WR.

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

PMID:
10547837
33.

Evolution of protein sequences and structures.

Wood TC, Pearson WR.

J Mol Biol. 1999 Aug 27;291(4):977-95.

PMID:
10452901
34.

Generalized neighbor-joining: more reliable phylogenetic tree reconstruction.

Pearson WR, Robins G, Zhang T.

Mol Biol Evol. 1999 Jun;16(6):806-16.

PMID:
10368958
35.

Panning for genes--A visual strategy for identifying novel gene orthologs and paralogs.

Retief JD, Lynch KR, Pearson WR.

Genome Res. 1999 Apr;9(4):373-82.

36.

Distinctive structure of the human GSTM3 gene-inverted orientation relative to the mu class glutathione transferase gene cluster.

Patskovsky YV, Huang MQ, Takayama T, Listowsky I, Pearson WR.

Arch Biochem Biophys. 1999 Jan 1;361(1):85-93.

PMID:
9882431
38.

Empirical statistical estimates for sequence similarity searches.

Pearson WR.

J Mol Biol. 1998 Feb 13;276(1):71-84.

PMID:
9514730
39.

Characterization of the human class Mu glutathione S-transferase gene cluster and the GSTM1 deletion.

Xu S, Wang Y, Roe B, Pearson WR.

J Biol Chem. 1998 Feb 6;273(6):3517-27.

40.

Comparison of DNA sequences with protein sequences.

Pearson WR, Wood T, Zhang Z, Miller W.

Genomics. 1997 Nov 15;46(1):24-36.

PMID:
9403055
41.

Aligning a DNA sequence with a protein sequence.

Zhang Z, Pearson WR, Miller W.

J Comput Biol. 1997 Fall;4(3):339-49.

PMID:
9278064
42.

Identifying distantly related protein sequences.

Pearson WR.

Comput Appl Biosci. 1997 Aug;13(4):325-32. Review. No abstract available.

PMID:
9283747
43.

Effective protein sequence comparison.

Pearson WR.

Methods Enzymol. 1996;266:227-58.

PMID:
8743688
44.
45.

A new approach to primer selection in polymerase chain reaction experiments.

Pearson WR, Robins G, Wrege DE, Zhang T.

Proc Int Conf Intell Syst Mol Biol. 1995;3:285-91.

PMID:
7584448
46.

MIF proteins are not glutathione transferase homologs.

Pearson WR.

Protein Sci. 1994 Mar;3(3):525-7.

47.

Primary structure of avian H+/K(+)-ATPase beta-subunit.

Yu H, Ishii T, Pearson WR, Takeyasu K.

Biochim Biophys Acta. 1994 Feb 23;1190(1):189-92.

PMID:
8110815
48.

Using the FASTA program to search protein and DNA sequence databases.

Pearson WR.

Methods Mol Biol. 1994;24:307-31. No abstract available.

PMID:
8205202
49.

Using the FASTA program to search protein and DNA sequence databases.

Pearson WR.

Methods Mol Biol. 1994;25:365-89. No abstract available.

PMID:
8004177

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