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Rapid membrane protein topology prediction
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- Hennerdal, Aron, 1981- (author)
- Stockholms universitet,Institutionen för biokemi och biofysik,Arne Elofsson
-
- Elofsson, Arne (author)
- Stockholms universitet,Institutionen för biokemi och biofysik
- (creator_code:org_t)
- 2011-04-13
- 2011
- English.
- In: Bioinformatics. - : Oxford University Press (OUP). - 1367-4803 .- 1367-4811. ; 27:9, s. 1322-1323
- Journal article (peer-reviewed)
Abstract
Subject headings
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- State-of-the-art methods for topology of α-helical membrane proteins are based on the use of time-consuming multiple sequence alignments obtained from PSI-BLAST or other sources. Here, we examine if it is possible to use the consensus of topology prediction methods that are based on single sequences to obtain a similar accuracy as the more accurate multiple sequence-based methods. Here, we show that TOPCONS-single performs better than any of the other topology prediction methods tested here, but ~6% worse than the best method that is utilizing multiple sequence alignments. AVAILABILITY AND IMPLEMENTATION: TOPCONS-single is available as a web server from http://single.topcons.net/ and is also included for local installation from the web site. In addition, consensus-based topology predictions for the entire international protein index (IPI) is available from the web server and will be updated at regular intervals.
Subject headings
- NATURVETENSKAP -- Biologi -- Bioinformatik och systembiologi (hsv//swe)
- NATURAL SCIENCES -- Biological Sciences -- Bioinformatics and Systems Biology (hsv//eng)
Keyword
- Bioinformatics
- Bioinformatik
- Computing Science
- administrativ databehandling
- Molecular Biotechnology
- molekylär bioteknik (avd f jonfysik)
Publication and Content Type
- ref (subject category)
- art (subject category)
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