I have a bioinformatics program written in C that I would like to serve over the web. The application is currently run on the command line via a perl script that is able to process multiple files with different options and spits out R code to generate postscript graphs using the dotplot files. Input is two DNA sequences, 4 options (flags) and the output is two text files: a dotplot file (for graphing the alignment) and an alignment file (showing where the two sequences match).

I want to serve this app over the web using the standard CGI/PERL paradigm. The challeng is to make the graphs dynamic such that after mouse-over a feature on the graph will show the corresponding region in the alignment text file (or something similar). Clever perl scripting could be used to generate an html image map for the graphs as needed . I am open to other solutions though.