LogoBar : Bar graph visualization of protein logos with gaps

• 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.

Ämnesord

NATURVETENSKAP  -- Biologi -- Biokemi och molekylärbiologi (hsv//swe)

NATURAL SCIENCES  -- Biological Sciences -- Biochemistry and Molecular Biology (hsv//eng)

Nyckelord

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

Publikations- och innehållstyp

ref (ämneskategori)

art (ämneskategori)