Example of a secondary structure prediction using SSpro:

Query Name: TonB E.c.
Message-ID:  <200106280205.aa07537@gremlin-relay.ics.uci.edu>

Query Length: 243

Prediction:

MIMTSMTLDLPRRFPWPTLLSVCIHGAVVAGLLYTSVHQVIELPAPAQPISVTMVTPADL
CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCHHHHHCCCCCCCCEEEEEECCCCC


EPPQAVQPPPEPVVEPEPEPEPIPEPPKEAPVVIEKPKPKPKPKPKPVKKVQEQPKRDVK
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCEC


PVESRPASPFENTAPARLTSSTATAATSKPVTSVASGPRALSRNQPQYPARAQALRIEGQ
CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCCEE


VKVKFDVTPDGRVDNVQILSAKPANMFEREVKNAMRRWRYEPGKPGSGIVVNILFKINGT
EEEEEEECCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCCCCCCCCCCCEEEEEEEECCC


TEIQ
EECC


PSI-BLAST hits : 22


For an explanation of the formats see:
http://promoter.ics.uci.edu/BRNN-PRED/explanation.html#output_formats

SSpro2, SSpro8, ACCpro, CONpro can be found at: 
http://promoter.ics.uci.edu/BRNN-PRED/

Please cite:
Baldi,P., Brunak,S., Frasconi,P., Pollastri,G., Soda,G. (1999).
"Exploiting the past and the future in protein secondary structure prediction".
Bioinformatics, 15:937-946.
ftp://promoter.ics.uci.edu/Papers/1999_GTCB.ps.gz

Or:
Pollastri,G., Baldi,P., Fariselli,P., Casadio,R. (2001).
"Improved Prediction of the Number of Residue Contacts in Proteins by Recurrent Neural Networks".
Bioinformatics (ISMB2001 special issue), in press.
ftp://promoter.ics.uci.edu/Papers/2001_ISMB.ps.gz

Query served in 205 seconds

Latest update of content: June 28, 2001

Ralf Koebnik
Institut de recherche pour le dèveloppement
UMR 5096, CNRS-UP-IRD
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