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.
| Identifer | oai:union.ndltd.org:UPSALLA1/oai:DiVA.org:su-61921 |
| Date | January 2011 |
| Creators | Hennerdal, Aron, Elofsson, Arne |
| Publisher | Stockholms universitet, Institutionen för biokemi och biofysik, Stockholms universitet, Institutionen för biokemi och biofysik |
| Source Sets | DiVA Archive at Upsalla University |
| Language | English |
| Detected Language | English |
| Type | Article in journal, info:eu-repo/semantics/article, text |
| Format | application/pdf |
| Rights | info:eu-repo/semantics/openAccess |
| Relation | Bioinformatics, 1367-4803, 2011, 27:9, s. 1322-1323, info:eu-repo/grantAgreement/EC/FP7/512092; 201924 |
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