[EMBOSS] EMBOSS interface for InsightII

[Kimmo Mattila]

Hi,

I have written a set of scripts to create a simple EMBOSS interface to 
insightII molecular modeling program. InsightII is a commercial 
molecular modeling program by Acclerys so it is not freely available.
However, if you have InsightII and EMBOSS installed to your 
machine and you wish to test the EMBOSS interface, please feel free to 
download the scripts from URL:

http://www.csc.fi/chem/progs/insightII_csc.phtml.en#EMBOSS

The insight_EMBOSS.tar file, which you can download from the URL above, 
contains a README that describes the installation process. In the best 
case all you need to do is to set up your insightII environment and run 
an installation script.

When the scripts are installed, an EMBOSS menu will appear to your 
Homology module menu list. Note that you can apply EMBOSS commands only 
to those sequences that have been read in into the sequence window of 
insightII. The only exception to this is seqret, which you can use to 
read sequences to the sequence window. The results can be used to create 
plots, color residue regions or to define atom subsets.

The InsightII EMBOSS interface is focused to those EMBOSS tools, that do 
not have a counterpart in InsightII. The homology modeling module of 
insightII includes for example sequence alignment tools and thus programs 
like needle or water are not included. At the moment interface scripts are 
available for following EMBOSS programs:

   antigenic
   charge
   digest
   dotmatcher
   fuzzpro
   helixturnhelix
   hmoment
   iep
   infoalign
   octanol
   patmatmotifs
   pepinfo
   pepnet
   pepstats
   pepwheel
   plotcon
   polydot
   prettyplot
   seqret
   sigcleave
   tmap

Any comments and suggestions about the interface are welcome but please 
remember that the scripts are not produced by any official programming 
project. They are just a kind of side product of a research project.

Regards,

Kimmo Mattila



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Kimmo Mattila, sovellusasiantuntija, Bioinformatiikan palvelut, CSC
PL 405 02101 Espoo, puh 09 457 2708 , fax (09) 457 2302
CSC on tieteen tietotekniikan keskus, www.csc.fi, s-posti: 
kimmo.mattila at csc.fi

Kimmo Mattila, application scientist, Bioinformatics Support, CSC
P.O. Box 405 02101 Espoo, Finland, tel +358 9 4572708, fax +358 9 4572302
CSC is the Finnish IT Center for Science, www.csc.fi, e-mail: 
kimmo.mattila at csc.fi
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