SimiTri--visualizing similarity relationships for groups of sequences.
Global sequence comparisons between large datasets, such as those arising from genome projects, can be problematic to display and analyze. We have developed SimiTri, a Java/Perl-based application, which allows simultaneous display and analysis of relative similarity relationships of the dataset of interest to three different databases. We illustrate its utility in identifying Caenorhabditis elegans genes that have distinct patterns of phylogenetic affinity suggestive of horizontal gene transfer. SimiTri is freely downloadable from http://www.nematodes.org/SimiTri/ and the source code is freely available from the authors.
Parkinson
John
J
Institute of Cell, Animal and Population Biology, University of Edinburgh, Edinburgh EH9 3JT, UK. john.parkinson@ed.ac.uk
Blaxter
Mark
M
D000818:Animals; D017173:Caenorhabditis elegans / Q000235:genetics / Q000378:metabolism; D029742:Caenorhabditis elegans Proteins / Q000235:genetics; D003628:Database Management Systems; D030562:Databases, Protein; D004330:Drosophila / Q000235:genetics / Q000378:metabolism; D029721:Drosophila Proteins / Q000235:genetics / Q000378:metabolism; D022761:Gene Transfer, Horizontal / Q000235:genetics; D006801:Humans; D010802:Phylogeny; D011506:Proteins / Q000235:genetics* / Q000378:metabolism; D012441:Saccharomyces cerevisiae / Q000235:genetics / Q000378:metabolism; D016415:Sequence Alignment / Q000379:methods*; D017422:Sequence Analysis, DNA / Q000379:methods*; D017386:Sequence Homology, Amino Acid; D013045:Species Specificity; D014584:User-Computer Interface
D029742:Caenorhabditis elegans Proteins; D029721:Drosophila Proteins; D011506:Proteins