LogoBar is a Java application created to deal with the legibility problems of existing sequence logo software. Today when a sequence logo is created it is hard to read characters that have either been stretched out due to high residue conservation at a position, or very compressed characters due to high variability at a position in the alignment. The second problem is a bigger issue in protein sequence alignments than in alignments consisting of nucleotide sequences since the first type of alignment can have up to 20 characters displayed at the same position. The second type of logo can maximum have four characters per position. For this reason LogoBar was prioritized to only deal with protein
multiple alignments. In LogoBar instead of displaying the residues as characters a graph consisting of bars is created. To distinguish between the different amino acids the one letter abbreviation for the amino acids are displayed inside its corresponding bar. Moreover, LogoBar displays the gaps as well. The one letter abbreviation for these are ’-’. Gaps are calculated just like any other residue in the alignment, and therefore the original sequence logo calculations have been modified. LogoBar parses Clustal aln files, and automatically creates an output.txt file with data from the statistical calculations performed. Furthermore, the user can choose to save the graph as an EPS image file under an optional name. |