transmembrane spans for an entire genome

Arne Elofsson arne at
Fri Dec 19 00:26:03 EST 1997

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toddc.NoSpAm at (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 

> 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 ?

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.


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              The more I use Windows, the more I love Linux
 Arne Elofsson     arne at
 Tel:+46(0)8-161553      Dept of Biochemistry, Stockholm University
 Fax:+46(0)8-153679	 10691 Stockholm, Sweden


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