PhyloDome--visualization of taxonomic distributions of domains occurring in eukaryote protein sequence sets.
The analysis of taxonomic distribution and lineage-specific variation of domains and domain combinations is an important step in the assessment of their functional roles and potential interoperability. In the study of eukaryote sequence sets with many multi-domain proteins, it can become laborious to evaluate the phylogenetic context of the many occurring domains and their mutual relationships. PhyloDome is an answer to that problem. It provides a fast overview on the taxonomic spreading and potential interrelation of domains that are either given as a list of names and PFAM/SMART accessions or derived from a user-defined set of sequences. This taxonomic distribution analysis can be helpful in protein function and interaction assignment as the comparative study of potential Hedgehog pathway members in C.elegans shows. An implementation of PhyloDome is accessible for public use as a WWW-Service at http://mendel.imp.univie.ac.at/phylodome/. Software components are available on request.
Novatchkova
Maria
M
Gregor-Mendel-Institute (GMI) of the Austrian Academy of Sciences, Dr Ignaz Seipel-Platz 2, A-1010 Vienna, Austria. novatchkova@imp.univie.ac.at
Wildpaner
Michael
M
Schweizer
Dieter
D
Eisenhaber
Frank
F
D000818:Animals; D017173:Caenorhabditis elegans / Q000378:metabolism; D029742:Caenorhabditis elegans Proteins / Q000737:chemistry / Q000145:classification; D003196:Computer Graphics; D029721:Drosophila Proteins / Q000737:chemistry / Q000145:classification; D005057:Eukaryotic Cells / Q000737:chemistry; D020407:Internet; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D011506:Proteins / Q000145:classification*; D020539:Sequence Analysis, Protein; D015398:Signal Transduction; D012984:Software
D029742:Caenorhabditis elegans Proteins; D029721:Drosophila Proteins; D011506:Proteins