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Results: 1 to 20 of 80

1.

MatrixPlot: visualizing sequence constraints.

Gorodkin J, Staerfeldt HH, Lund O, Brunak S.

Bioinformatics. 1999 Sep;15(9):769-70.

PMID:
10498780
[PubMed - indexed for MEDLINE]
Free Article
2.

InterMap3D: predicting and visualizing co-evolving protein residues.

Gouveia-Oliveira R, Roque FS, Wernersson R, Sicheritz-Ponten T, Sackett PW, Mølgaard A, Pedersen AG.

Bioinformatics. 2009 Aug 1;25(15):1963-5. doi: 10.1093/bioinformatics/btp335. Epub 2009 Jun 15.

PMID:
19528088
[PubMed - indexed for MEDLINE]
Free Article
3.

Displaying the information contents of structural RNA alignments: the structure logos.

Gorodkin J, Heyer LJ, Brunak S, Stormo GD.

Comput Appl Biosci. 1997 Dec;13(6):583-6.

PMID:
9475985
[PubMed - indexed for MEDLINE]
4.

transAlign: using amino acids to facilitate the multiple alignment of protein-coding DNA sequences.

Bininda-Emonds OR.

BMC Bioinformatics. 2005 Jun 22;6:156.

PMID:
15969769
[PubMed - indexed for MEDLINE]
Free PMC Article
5.

Seq2Logo: a method for construction and visualization of amino acid binding motifs and sequence profiles including sequence weighting, pseudo counts and two-sided representation of amino acid enrichment and depletion.

Thomsen MC, Nielsen M.

Nucleic Acids Res. 2012 Jul;40(Web Server issue):W281-7. doi: 10.1093/nar/gks469. Epub 2012 May 25.

PMID:
22638583
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

GeneWiz browser: An Interactive Tool for Visualizing Sequenced Chromosomes.

Hallin PF, Stærfeldt HH, Rotenberg E, Binnewies TT, Benham CJ, Ussery DW.

Stand Genomic Sci. 2009 Sep 25;1(2):204-15. doi: 10.4056/sigs.28177.

PMID:
21304658
[PubMed]
Free PMC Article
7.

Multiple sequence alignment with user-defined constraints at GOBICS.

Morgenstern B, Werner N, Prohaska SJ, Steinkamp R, Schneider I, Subramanian AR, Stadler PF, Weyer-Menkhoff J.

Bioinformatics. 2005 Apr 1;21(7):1271-3. Epub 2004 Nov 16.

PMID:
15546937
[PubMed - indexed for MEDLINE]
Free Article
8.

ViTO: tool for refinement of protein sequence-structure alignments.

Catherinot V, Labesse G.

Bioinformatics. 2004 Dec 12;20(18):3694-6. Epub 2004 Jul 22.

PMID:
15271783
[PubMed - indexed for MEDLINE]
Free Article
9.

Evolutionary divergence plots of homologous proteins.

Brouillet S, Risler JL, Hénaut A, Slonimski PP.

Biochimie. 1992 Jun;74(6):571-80.

PMID:
1520737
[PubMed - indexed for MEDLINE]
10.

APDB: a web server to evaluate the accuracy of sequence alignments using structural information.

Armougom F, Poirot O, Moretti S, Higgins DG, Bucher P, Keduas V, Notredame C.

Bioinformatics. 2006 Oct 1;22(19):2439-40.

PMID:
17032685
[PubMed - indexed for MEDLINE]
Free Article
11.

ProBias: a web-server for the identification of user-specified types of compositionally biased segments in protein sequences.

Kuznetsov IB.

Bioinformatics. 2008 Jul 1;24(13):1534-5. doi: 10.1093/bioinformatics/btn233. Epub 2008 May 14.

PMID:
18480099
[PubMed - indexed for MEDLINE]
Free Article
12.

NESbase version 1.0: a database of nuclear export signals.

la Cour T, Gupta R, Rapacki K, Skriver K, Poulsen FM, Brunak S.

Nucleic Acids Res. 2003 Jan 1;31(1):393-6.

PMID:
12520031
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

JAE: Jemboss Alignment Editor.

Carver TJ, Mullan LJ.

Appl Bioinformatics. 2005;4(2):151-4.

PMID:
16128618
[PubMed - indexed for MEDLINE]
14.

Combining many multiple alignments in one improved alignment.

Bucka-Lassen K, Caprani O, Hein J.

Bioinformatics. 1999 Feb;15(2):122-30.

PMID:
10089197
[PubMed - indexed for MEDLINE]
Free Article
15.

Using CLUSTAL for multiple sequence alignments.

Higgins DG, Thompson JD, Gibson TJ.

Methods Enzymol. 1996;266:383-402.

PMID:
8743695
[PubMed - indexed for MEDLINE]
16.

MaxSubSeq: an algorithm for segment-length optimization. The case study of the transmembrane spanning segments.

Fariselli P, Finelli M, Marchignoli D, Martelli PL, Rossi I, Casadio R.

Bioinformatics. 2003 Mar 1;19(4):500-5.

PMID:
12611805
[PubMed - indexed for MEDLINE]
Free Article
17.

DBAli: a database of protein structure alignments.

Martí-Renom MA, Ilyin VA, Sali A.

Bioinformatics. 2001 Aug;17(8):746-7.

PMID:
11524379
[PubMed - indexed for MEDLINE]
Free Article
18.

ProfileGrids as a new visual representation of large multiple sequence alignments: a case study of the RecA protein family.

Roca AI, Almada AE, Abajian AC.

BMC Bioinformatics. 2008 Dec 22;9:554. doi: 10.1186/1471-2105-9-554.

PMID:
19102758
[PubMed - indexed for MEDLINE]
Free PMC Article
19.

POAVIZ: a Partial order multiple sequence alignment visualizer.

Grasso C, Quist M, Ke K, Lee C.

Bioinformatics. 2003 Jul 22;19(11):1446-8.

PMID:
12874062
[PubMed - indexed for MEDLINE]
Free Article
20.

ALIGN_MTX--an optimal pairwise textual sequence alignment program, adapted for using in sequence-structure alignment.

Vishnepolsky B, Pirtskhalava M.

Comput Biol Chem. 2009 Jun;33(3):235-8. doi: 10.1016/j.compbiolchem.2009.04.003. Epub 2009 May 3.

PMID:
19477686
[PubMed - indexed for MEDLINE]

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