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software to remove redundant proteins

PIR help at uniprot.org
Fri Jan 23 14:41:57 EST 2004


Dear Florent,
An alternative to using a software redundancy can also be reduced by 
using BLAST against non-redundant databases such as UniRef100, UniRef90 
or UniRef50. The UniRef databases combine closely related sequences into 
a single record thereby hiding fragments and other identical sequences 
from the BLAST results. From the BLAST result page you can still view 
all the collapsed sequences by clicking on the UniRef ID. You can BLAST 
UniRef databases at http://www.pir.uniprot.org/search/blast.shtml. 
UniRef databases are part of UniProt (Universal Protein Resource) which 
is a central repository of protein sequence and function created by 
joining the information contained in Swiss-Prot, TrEMBL, and PIR 
(http://www.uniprot.org).
Best regards,
Raja

florent.crepineau wrote:

Subject: software to remove redundant proteins
From: florent.crepineau at laposte.net ("florent.crepineau")
Date: Mon, 12 Jan 2004 17:01:43 +0000 (GMT)
To: bionet-software at net.bio.net
Newsgroups: bionet.software

Hello and happy new year,

After a BLAST, many sequences are indeed the same (fragments,
update, different names....). I am looking for a software to
reduce the redundancy of this set of protein.

Thank you in advance.

Best regards

Dr Florent Crépineau


-- 
Raja Mazumder
Scientific Coordinator, Protein Information Resource
Assistant Professor, Department of Biochemistry and Molecular Biology
Georgetown University Medical Center
3900 Reservoir Rd., PCS bldg LR3
Washington, D.C. 20057-1414
Phone: (202) 6879970
Fax: (202) 6871662





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