ABCC : Application's document Page

SeqSpace At ABCC
Name: 
Sequence Space
Version(s): 


Category:

Protein Analysis, Sequence Analysis, Bioinformatics


Author(s)/Vendor(s):

Chris Dodge, Chris Sander
EMBL - EBI 



Program Description:

Sequence Space implements a method of clustering aligned protein
sequences based upon the algorithm developed by G. Casari, C. Sander
and A. Valencia. Full details of the method can be found in the
paper: A method to predict functional residues in proteins, Georg
Casari, Chris Sander and Alfonso Valencia. Structural Biology volume
2, no. 2, February 1995. 

Each sequence is converted into a vector in "Sequence Space",
projection of which onto a lower dimensional space allows 2- or
3-dimensional viewing of the resulting clusters. 

By projecting the sequence residues into the same space, groups of
residues specific for the clusters are revealed, allowing the
identification of residues that are predicted to be directly
involved in protein function. 

There are two programs available, the main sequence space program
and a set of Java viewers combining sequence space views
with more conventional protein displays.  



Computer platform(s):

SGI 



Location:

/usr/local/fbscapp/SequenceSpace 



Access:

To run Sequence Space:
alias seqspace /usr/local/fbscapp/SequenceSpace/SeqSpace

To start java viewers:
setenv CLASSPATH \
/usr/local/fbscapp/SequenceSpace/SeqSpace.jar
/usr/java/bin/java SeqSpace



Documentation:

http://industry.ebi.ac.uk/SeqSpace/UG.html



Web Site:

http://industry.ebi.ac.uk/SeqSpace/ 



ABCC Contact Person:

 



Created By:

miaskiew



Created Time:

2001-10-30


Updated By:

 




Updated Time:






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