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Items: 1 to 20 of 106

1.

CodonLogo: a sequence logo-based viewer for codon patterns.

Sharma V, Murphy DP, Provan G, Baranov PV.

Bioinformatics. 2012 Jul 15;28(14):1935-6. doi: 10.1093/bioinformatics/bts295.

2.

Skylign: a tool for creating informative, interactive logos representing sequence alignments and profile hidden Markov models.

Wheeler TJ, Clements J, Finn RD.

BMC Bioinformatics. 2014 Jan 13;15:7. doi: 10.1186/1471-2105-15-7.

3.

LogoBar: bar graph visualization of protein logos with gaps.

Pérez-Bercoff A, Koch J, Bürglin TR.

Bioinformatics. 2006 Jan 1;22(1):112-4.

PMID:
16269415
4.

WebLogo: a sequence logo generator.

Crooks GE, Hon G, Chandonia JM, Brenner SE.

Genome Res. 2004 Jun;14(6):1188-90.

5.

Log-odds sequence logos.

Yu YK, Capra JA, Stojmirović A, Landsman D, Altschul SF.

Bioinformatics. 2015 Feb 1;31(3):324-31. doi: 10.1093/bioinformatics/btu634.

6.

enoLOGOS: a versatile web tool for energy normalized sequence logos.

Workman CT, Yin Y, Corcoran DL, Ideker T, Stormo GD, Benos PV.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W389-92.

7.

Two Sample Logo: a graphical representation of the differences between two sets of sequence alignments.

Vacic V, Iakoucheva LM, Radivojac P.

Bioinformatics. 2006 Jun 15;22(12):1536-7.

PMID:
16632492
8.
9.

BLogo: a tool for visualization of bias in biological sequences.

Li W, Yang B, Liang S, Wang Y, Whiteley C, Cao Y, Wang X.

Bioinformatics. 2008 Oct 1;24(19):2254-5. doi: 10.1093/bioinformatics/btn407.

PMID:
18682425
10.

ARCS: an aggregated related column scoring scheme for aligned sequences.

Song B, Choi JH, Chen G, Szymanski J, Zhang GQ, Tung AK, Kang J, Kim S, Yang J.

Bioinformatics. 2006 Oct 1;22(19):2326-32.

PMID:
16870930
11.

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
12.

Mulan: multiple-sequence local alignment and visualization for studying function and evolution.

Ovcharenko I, Loots GG, Giardine BM, Hou M, Ma J, Hardison RC, Stubbs L, Miller W.

Genome Res. 2005 Jan;15(1):184-94.

13.

28-way vertebrate alignment and conservation track in the UCSC Genome Browser.

Miller W, Rosenbloom K, Hardison RC, Hou M, Taylor J, Raney B, Burhans R, King DC, Baertsch R, Blankenberg D, Kosakovsky Pond SL, Nekrutenko A, Giardine B, Harris RS, Tyekucheva S, Diekhans M, Pringle TH, Murphy WJ, Lesk A, Weinstock GM, Lindblad-Toh K, Gibbs RA, Lander ES, Siepel A, Haussler D, Kent WJ.

Genome Res. 2007 Dec;17(12):1797-808.

14.

Interactive software tool to comprehend the calculation of optimal sequence alignments with dynamic programming.

Ibarra IL, Melo F.

Bioinformatics. 2010 Jul 1;26(13):1664-5. doi: 10.1093/bioinformatics/btq252.

16.

ESPERR: learning strong and weak signals in genomic sequence alignments to identify functional elements.

Taylor J, Tyekucheva S, King DC, Hardison RC, Miller W, Chiaromonte F.

Genome Res. 2006 Dec;16(12):1596-604.

17.

Pattern locator: a new tool for finding local sequence patterns in genomic DNA sequences.

Mrázek J, Xie S.

Bioinformatics. 2006 Dec 15;22(24):3099-100.

PMID:
17095514
18.

Fast model-based protein homology detection without alignment.

Hochreiter S, Heusel M, Obermayer K.

Bioinformatics. 2007 Jul 15;23(14):1728-36.

PMID:
17488755
19.

MACSE: Multiple Alignment of Coding SEquences accounting for frameshifts and stop codons.

Ranwez V, Harispe S, Delsuc F, Douzery EJ.

PLoS One. 2011;6(9):e22594. doi: 10.1371/journal.pone.0022594.

20.

PSAT: a web tool to compare genomic neighborhoods of multiple prokaryotic genomes.

Fong C, Rohmer L, Radey M, Wasnick M, Brittnacher MJ.

BMC Bioinformatics. 2008 Mar 26;9:170. doi: 10.1186/1471-2105-9-170.

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