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Items: 1 to 20 of 113

1.

pLogo: a probabilistic approach to visualizing sequence motifs.

O'Shea JP, Chou MF, Quader SA, Ryan JK, Church GM, Schwartz D.

Nat Methods. 2013 Dec;10(12):1211-2. doi: 10.1038/nmeth.2646. Epub 2013 Oct 6.

PMID:
24097270
2.

Discriminative motif finding for predicting protein subcellular localization.

Lin TH, Murphy RF, Bar-Joseph Z.

IEEE/ACM Trans Comput Biol Bioinform. 2011 Mar-Apr;8(2):441-51. doi: 10.1109/TCBB.2009.82.

3.

A generalized affine gap model significantly improves protein sequence alignment accuracy.

Zachariah MA, Crooks GE, Holbrook SR, Brenner SE.

Proteins. 2005 Feb 1;58(2):329-38.

PMID:
15562515
4.

3MOTIF: visualizing conserved protein sequence motifs in the protein structure database.

Bennett SP, Nevill-Manning CG, Brutlag DL.

Bioinformatics. 2003 Mar 1;19(4):541-2.

6.
7.

PrDOS: prediction of disordered protein regions from amino acid sequence.

Ishida T, Kinoshita K.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W460-4. Epub 2007 Jun 12.

8.

Phylomat: an automated protein motif analysis tool for phylogenomics.

Graham WV, Tcheng DK, Shirk AL, Attene-Ramos MS, Welge ME, Gaskins HR.

J Proteome Res. 2004 Nov-Dec;3(6):1289-91.

PMID:
15595740
9.

Probabilistic alignment of motifs with sequences.

Gonnet P, Lisacek F.

Bioinformatics. 2002 Aug;18(8):1091-101.

11.
12.

Multiple Motif Scanning to identify methyltransferases from the yeast proteome.

Petrossian TC, Clarke SG.

Mol Cell Proteomics. 2009 Jul;8(7):1516-26. doi: 10.1074/mcp.M900025-MCP200. Epub 2009 Apr 7.

13.
14.

Computing the P-value of the information content from an alignment of multiple sequences.

Nagarajan N, Jones N, Keich U.

Bioinformatics. 2005 Jun;21 Suppl 1:i311-8. Erratum in: Bioinformatics. 2005 Sep 15;21(18):3700.

15.

CompariMotif: quick and easy comparisons of sequence motifs.

Edwards RJ, Davey NE, Shields DC.

Bioinformatics. 2008 May 15;24(10):1307-9. doi: 10.1093/bioinformatics/btn105. Epub 2008 Mar 28.

16.

A study of statistical methods for function prediction of protein motifs.

Tao T, Zhai CX, Lu X, Fang H.

Appl Bioinformatics. 2004;3(2-3):115-24.

PMID:
15693737
17.

Structural alphabet motif discovery and a structural motif database.

Ku SY, Hu YJ.

Comput Biol Med. 2012 Jan;42(1):93-105. doi: 10.1016/j.compbiomed.2011.10.013. Epub 2011 Nov 17.

PMID:
22099701
18.

DOMAC: an accurate, hybrid protein domain prediction server.

Cheng J.

Nucleic Acids Res. 2007 Jul;35(Web Server issue):W354-6. Epub 2007 Jun 6.

19.

Improving the alignment quality of consistency based aligners with an evaluation function using synonymous protein words.

Lin HN, Notredame C, Chang JM, Sung TY, Hsu WL.

PLoS One. 2011;6(12):e27872. doi: 10.1371/journal.pone.0027872. Epub 2011 Dec 2.

20.

Large-scale database searching using tandem mass spectra: looking up the answer in the back of the book.

Sadygov RG, Cociorva D, Yates JR 3rd.

Nat Methods. 2004 Dec;1(3):195-202. Review.

PMID:
15789030
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