Literature DB >> 10498780

MatrixPlot: visualizing sequence constraints.

J Gorodkin1, H H Staerfeldt, O Lund, S Brunak.   

Abstract

UNLABELLED: MatrixPlot is a program for making high-quality matrix plots, such as mutual information plots of sequence alignments and distance matrices of sequences with known three-dimensional coordinates. The user can add information about the sequences (e.g. a sequence logo profile) along the edges of the plot, as well as zoom in on any region in the plot. AVAILABILITY: MatrixPlot can be obtained on request, and can also be accessed online at http://www. cbs.dtu.dk/services/MatrixPlot. CONTACT: gorodkin@cbs.dtu.dk

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Year:  1999        PMID： 10498780     DOI： 10.1093/bioinformatics/15.9.769

Source DB:  PubMed          Journal:  Bioinformatics        ISSN： 1367-4803            Impact factor:   6.937


  15 in total

1.  Comparative analysis of secondary structure of insect mitochondrial small subunit ribosomal RNA using maximum weighted matching.

Authors:  R D Page
Journal:  Nucleic Acids Res       Date:  2000-10-15       Impact factor: 16.971

2.  Discovering common stem-loop motifs in unaligned RNA sequences.

Authors:  J Gorodkin; S L Stricklin; G D Stormo
Journal:  Nucleic Acids Res       Date:  2001-05-15       Impact factor: 16.971

3.  Bacterial DNA uptake sequences can accumulate by molecular drive alone.

Authors:  H Maughan; L A Wilson; R J Redfield
Journal:  Genetics       Date:  2010-07-13       Impact factor: 4.562

4.  Cardioviral RNA structure logo analysis: entropy, correlations, and prediction.

Authors:  Xiao-Zhou Chen; Huai Cao; Wen Zhang; Ci-Quan Liu
Journal:  J Biol Phys       Date:  2009-08-29       Impact factor: 1.365

5.  A statistical test for conserved RNA structure shows lack of evidence for structure in lncRNAs.

Authors:  Elena Rivas; Jody Clements; Sean R Eddy
Journal:  Nat Methods       Date:  2016-11-07       Impact factor: 28.547

Review 6.  From structure prediction to genomic screens for novel non-coding RNAs.

Authors:  Jan Gorodkin; Ivo L Hofacker
Journal:  PLoS Comput Biol       Date:  2011-08-04       Impact factor: 4.475

7.  Parallel evolution of the genetic code in arthropod mitochondrial genomes.

Authors:  Federico Abascal; David Posada; Robin D Knight; Rafael Zardoya
Journal:  PLoS Biol       Date:  2006-04-25       Impact factor: 8.029

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

Authors:  Christopher T Workman; Yutong Yin; David L Corcoran; Trey Ideker; Gary D Stormo; Panayiotis V Benos
Journal:  Nucleic Acids Res       Date:  2005-07-01       Impact factor: 16.971

9.  CorreLogo: an online server for 3D sequence logos of RNA and DNA alignments.

Authors:  Eckart Bindewald; Thomas D Schneider; Bruce A Shapiro
Journal:  Nucleic Acids Res       Date:  2006-07-01       Impact factor: 16.971

10.  Finding coevolving amino acid residues using row and column weighting of mutual information and multi-dimensional amino acid representation.

Authors:  Rodrigo Gouveia-Oliveira; Anders G Pedersen
Journal:  Algorithms Mol Biol       Date:  2007-10-03       Impact factor: 1.405
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