ABCC : Application's document Page

CoreSearch At ABCC
Name: 
CoreSearch
Version(s): 
1.3
Category: 
Gene Regulation, Sequence Analysis, Bioinformatics
Author(s)/Vendor(s): 
F. Wolfertstetter, K. Frech, T. Werner
GSF - Institut fuer Saeugetiergenetik
AG BIODV
Ingolstaedter Landstr.1, 85764 Oberschleissheim, Germany
E-mail: frech@gsf.de
Program Description: 
CoreSearch is used to identify and delimitate unknown consensus elements
 (e.g. protein binding sites) in a set of unaligned DNA sequences. CoreSearch 
starts with a search for n-tuples (default n = 7) which occur in all or 
almost all of the sequences. In most cases
this initial search defines more than one 
tuple. Consecutive selection steps are employed in order to reduce the number of tuple candidates as soon as possible. The 
selection is based on maximization of the information content (consensus index), 
first of the n-tuple, and then of regions around the tuple.

The program ConsInspector can be used to scan new sequences for matches to the 
detected binding site. Multiple independent elements can be detected in 
successive program runs.

The program follows the methods described in Wolfertstetter,F., Frech,K., 
Herrmann,G., Werner,T. "Identification of functional elements in unaligned nucleic 
acid sequences by a novel tuple search algorithm", Comp. Appl. Biosci. 12, 71-80 (1996).
Computer platform(s): 
SGI Irix
Location: 
/usr/local/fbscapp/coresearch_1.3
Access: 
Account on SGI systems at ABCC is required.

When using C-shell:
 set path = ($path /usr/local/fbscapp/coresearch_1.3)
 coresearch
Documentation: 
User guide available in the text format:
/usr/local/fbscapp/coresearch_1.3/coresearch.doc
Web Site: 
http://anthea.gsf.de/biodv/consinspector.html
ABCC Contact Person: 
Sarangan Ravichandran
sravi@ncifcrf.gov
301-8461991
Created By: 
miaskiew
Created Time: 
2002-05-24
Updated By: 
miaskiew
Updated Time: 
2004-11-05
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