Neural Network programs for sequence analysis?

PARSONS_A at uk.co.pcr.snd01 PARSONS_A at uk.co.pcr.snd01
Thu Sep 2 08:49:22 EST 1993


In article <9308311856.AA03849 at genetics.com> mcolbert at GENETICS.COM writes:
>Hello,
>
>I am looking for information on neural network packages that can be used for
>protein and nucleic acid sequence analysis.  Specifically, we have novel
>sequences and want to see what (if anything) they may be similar to within the 
>databases.  The colleague I am asking this question for has already run 
>traditional types of homology searches (blast,fasta) with not much success.  
>The profile analysis offered in the GCG package is more sensitive than a 
>traditional homology search, but creating a profile requires having multiple 
>sequences that you align and search with, and we have only one sequence at a
>time.  I have done some work with neural networks (very limited) so we
>thought we would at least ask around.
>
>Any ideas?
>
>Thanks.
>
>-Maureen Colbert
>mcolbert at genetics.com

I know of two neural net applications ;-

Dmitrij Frishmann & Patrick Argos (1992)
"Recognition of distantly related protein sequences using conserved Motifs and 
 Neural Nets"

Jonathan Hirst & Michael Sternberg (1992)
"Evaluation of protein motif recognition by neural networks"

Both presented at "Genes, Proteins and Computers - 2nd International Conference
on Computing in Molecular Biology"  Chester (UK), September 1992

Frishmann at the time was at EMBL and a netfind shows him to be reachable as :

frishman at embl-heidelberg.de

also Argos can be mailed at:

argos at embl-heidelberg.de

I couldnt narrow down the icrf search theree are 27 domains at icrf - try
posting to postmaster at icrf.ac.uk they may be able to give you Hirst and Sternberg's
email addresses.

Bon Chance!

Tony P. (mbpcr at seqnet.dl.ac.uk AKA parsons_a at snd01.pcr.co.uk)




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