SimiTri

SimiTri is a new tool currently being developed which displays the the phylogenetic profiles for a large number of clusters on one graphic (see examples below). It has recently been made available to view selections of clusters from the annotationsearch page. How it works For each cluster, the consensus sequence was BLASTXed against a range of different protein databases - Archaebacteria, Drosophila, Saccharomyces cerevisiae, C. elegans, Mus musculus, Plasmodium falciparum, Xenopus laevis, Danio rerio, Eubacteria, Nematodes incl. C.elegans, Nematodes excl. C.elegans and Non nematode proteins. BLAST scores in excess of 50 (our 'significance cutoff') were extracted in addition to the highest e-value and imported into NEMBASE. SimiTri takes these values and uses them to draw a graphic in the form of a three-node graph. To launch the SimiTri application, simply select SimiTri under the output options and select the three databases to be used for making the comparisons. The selected clusters will then be used to generate a graphic and a list of clusters (see below). From the above figure it can be seen that each node of the triangle represents one set of sequences - C.elegans proteins, non-elegans nematode proteins and non-nematode proteins. The position of a cluster (represented as a single square coloured by the highest BLAST e-value) thus represents its relatedness to each of the three categories (calculated from the mean of the BLAST scores). The diagram below shows how the triangle may be interpreted. Clusters found on the three vertices indicate that they do not have a significant blast hit against the database located on the opposite node. Clusters which were found to be unique (no significant blast score against the three dbs) and those which only had a significant score for one database, are listed in a table below the graphic.