RHIMS BLAST visualisation

RHIMS (Relative Homology Index using Mathematical Summation) is a graphical analysis that provides a visual plot of how similar a query sequence is to a sequence database. High scoring pairwise matches from the search (in this case a BLAST search) are rescored, aggregated and plotted along the sequence length. This gives a sequence position dependent score of the similarity to the target database.

Whilst this may be interesting for a sequence as a whole, it becomes more useful when applied to subsets of the search results. Subsets could be selected by eg. keyword mining of the description field for each hit ('Select all hits with kinase in the description field'), giving the potential for the localisation of functionality on the sequence. Another benefit is that potentially uninformative matches are excluded ('BAC clone XXXYY from Some species 23456 bp').

A webserver is available here. It will process the output from blastall or blastcl3 using Bio::Tools::BPlite from the BioPerl toolkit and start up the applet. Your results will be retained on the server for a period of time.

Here are some examples [example 1] [example 2].

The applet requires Java2 in order to run. We have noticed problems with Internet Explorer on Windows XP when using the Microsoft Virtual Machine but not with the Sun Java Virtual Machine. Both Opera and Mozilla work fine with the Sun JVM.

Yes. The source is being made available under the General Public License. Please contact Dr David Martin for the source for the applet (Java2) and the server code (Perl, requires BioPerl).

We are actively improving the tools we use to visualise database searches and would welcome helpful comments. Please do let us know if you find this tool useful. We would encourage you to download the applet and use it locally. If you make modifications to this tool then please let us know so we can improve our version as well. An application note has been published in Bioinformatics. If you use this application to assist in work that is subsequently published, please cite Martin, D.M.A, Hill, P., Barton, G.J. and Flavell, A.J. (2003) Bioinformatics 19, 1037-1038.