transmembrane spans for an entire genome

[Arne Elofsson]

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toddc.NoSpAm at NoSpAm.anet-dfw.com (Todd C.) writes:

> I am interested in reviewing transmembrane spans for all the proteins
> across an entire genome such as M. Jannaschii or H. Pylori. 
> 
> I've looked at Rost's (PHDtopology) and Persson's (TMAP) and
> Frishman's (Predator) programs and all appear to require mulitple
> aligned homologous sequences for accuracy > 65%. 
> 

Toppred2 and DAS perform better on single sequences (available on
http://www.biokemi.su.se/~server/ 

> Rost posted transmembrane data for 4 genomes but omitted proteins with
> single spans from the result tables. 
> 
> Any recommendations for finding or generating transmembrane span
> predictions for the complete genomes stored at tigr.org ?
> 

Gunnar von Heijne and Erik Wallin have a paper in press in protein
science I think where they studied some ten genomes. There was a short
communication from Engelman and Brunger in Proteins a few month ago,
with very different results from the one in the Wallin study.

arne

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---------------------------------------------------------------------------
              The more I use Windows, the more I love Linux
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 Arne Elofsson     arne at bimbo.biokemi.su.se http://www.biokemi.su.se/~arne/
 Tel:+46(0)8-161553      Dept of Biochemistry, Stockholm University
 Fax:+46(0)8-153679	 10691 Stockholm, Sweden

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