Not a site for the paranormal; parasight is a program for visualizing and analyzing biological pairwise alignments. The program was initially designed to analyze the thousands of large segmental duplications found within the human genome. However, parasight's simple unassuming data model and flexible formatting allows for the display of virtually any pairwise alignment as well as formatting based on any ancillary data. It is most often used in the Eichler lab, to quickly analyze everyday BLAST searches of genomic sequence. More creative lab members have used it to analyze BAC end placements or the positions of insertional and deletional differences between primates species.
Parasight does not directly calculate alignments or specifically analyze the bases/residues of the involved sequences; rather it uses the coordinates to display the spatial relationships of alignments upon the involved sequences. Postscript output provides publication quality images. Parasight is written in Perl/Tk and is freely available. As mentioned parasight assumes very little about your data but can utilize almost any provided ancillary data. It also allows for further analysis (such as linking to external data and executing other programs.
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