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LogoBar: Bar graph visualization of protein logos with gaps
Södertörn University, School of Life Sciences. Karolinska Institute / Chalmers Universtiy.
Södertörn University, School of Life Sciences. Karolinska Institute.
Södertörn University, School of Life Sciences. Karolinska Institute.
2006 (English)In: Bioinformatics, ISSN 1367-4803, E-ISSN 1460-2059, Vol. 22, no 1, 112-114 p.Article in journal (Refereed) Published
Abstract [en]

Summary: LogoBar is a Java application to display protein sequence logos. In our software gaps are accounted for when calculating the information content present at each residue position in a multiple alignment. The resulting logo is displayed as a graph consisting of bars, although traditional letter representation is also possible. Amino acids are displayed from the bottom up with decreasing frequencies i.e. the most abundant residue is placed at the bottom of the logo. The bars can be color-coded according to user specifications. Gaps in the alignment are also displayed, either on top or at the bottom of the logo. Furthermore, residues can either be arranged according to their relative abundance or grouped according to user criteria to emphasize the conserved nature of particular positions.

Place, publisher, year, edition, pages
2006. Vol. 22, no 1, 112-114 p.
Keyword [en]
amino acid sequence, article, bioinformatics, computer program, genetic algorithm, information processing, priority journal, sequence alignment, Algorithms, Amino Acid Motifs, Amino Acids, Computational Biology, Computers, Conserved Sequence, Databases, Protein, Internet, Molecular Sequence Data, Programming Languages, Proteins, Sequence Analysis, Protein, Software
National Category
Biochemistry and Molecular Biology
Identifiers
URN: urn:nbn:se:sh:diva-22737DOI: 10.1093/bioinformatics/bti761ISI: 000234433500019PubMedID: 16269415ScopusID: 2-s2.0-30344446662OAI: oai:DiVA.org:sh-22737DiVA: diva2:715586
Available from: 2014-05-05 Created: 2014-03-13 Last updated: 2014-05-05Bibliographically approved

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Pérez-Bercoff, ÅsaKoch, JohanBürglin, Thomas R.
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