GRAPHICAL MULTIALIGNMENT FOR SGI AND PC
sbp at marvin.mr.sintef.no
Thu Jun 18 02:56:19 EST 1992
MULTIM - A graphical tool for multialignment
At the MR-Center in Trondheim we have a suite of programs for multialignment
of protein sequences (a package for DNA alignment will be coming later this
year). In the jungle of multialignment programs you may ask why yet another
package? One of the reasons for developing this package was that we would like
to avoid the uncertainties of cost penalties included in introducing gaps and deletions. Our software searches for local conserved motifs in a set of protein sequences (PIR format)- it creates a listing of such motifs and subsequently thesecan be screened for statistical significance. Finally the output is visualized in a graphical mode, as well as a postscript file that can be sent directly to your postscript printer (in color or B/W). You can now screen your data for conserved or similar motifs, and by s
imply inspecting the locations of these sites youcan identify possible insertions and deletions. We have identified cases where the size of such insertions reached 400 and 70 AA respectivel. It is unlikely that programs relying on gap penalties will indentify such large gaps (at least ifa gap-size dependent penalty is applied).
The graphical output can further be annotated with protein features such as
secondary structure (if such is available) or location of transmembrane segments etc.
If you are interested we are shipping MULTIM including manual at a price of 200 US$ for academic sites and 1000 US $ for commercial sites.
Steffen B. Petersen
Professor of Biostructure
FAX : 47-7-997708
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