Modifications SSP Genefinder service

Dan Davison dbd at THEORY.BCHS.UH.EDU
Tue Oct 25 10:22:16 EST 1994


      The Baylor College Of Medicine Computational Biology Group
			     Houston, TX
		       announces a new service

                                 SSP
       Prediction of a-helix and b-strand segments of globular
                               proteins

***************************************************************************
*********** NOTE ADDRESSES AND FORMATS HAVE CHANGED!! *********************
***************************************************************************

Analysis of uncharacterized human sequences is available by sending
a file containing a sequence name on the first line and sequence on
subsequent lines (no more than 80 char/line) to
(a sequence name in the first string)

                      service at bchs.uh.edu

 with the Subject line "SSP". 

Example: mail -s SSP service at bchs.uh.edu < test.seq

where test.seq a file with the sequence.

NOTE: This service is temporarily being provided through the
University of Houston Gene-Server.  Only two jobs will be run at a
time.
 
Method description:
**********************
   Our method is designed to locate secondary structure elements 
   and uses linear discriminant analysis to assign segments of a  
   given amino acid sequence to a particular type of secondary structure,
   by taking into account the amino acid composition of internal parts 
   of segments as well as their terminal and adjacent regions.
   Four linear discriminant functions were constructed for recognition 
   of short and long a-helix and b-strand segments, respectively. These 
   functions combine 3 characteristics: hydrophobic moment, segment 
   singlet and pair preferences to an a-helix or b-strand.  

Accuracy:
************************
   Overall 3-states (a, b, c) prediction gives ~65.1% correctly predic-
   ted residues on 126 non-homologous proteins using the jack-knife test
   procedure (The accuracy is good if you have no homologous sequences
   to apply Sander et al. method (Rost,Sander, Mol.Biol,1993,232,584-599)
   that has about 71% accuracy with using these sequences and about 61% 
   without them).
	Analysis of the prediction results shows a high 
   prediction accuracy of long secondary structure segments (~89% of a-
   helices of length greater than 8 and ~71% of b-strands of length 
   greater than 6 are correctly located with probability of correct
   prediction 0.82 and 0.78 respectively).

Submitting sequences via email:
***********************************
  For email submission the sequences must have the following format: 
  seqname 
  RLLRAIMGAPGSGKGTVSSRITKHFELKHLSSGDLLRDNMLRGTEIGVLA
  KTFIDQGKLIPDDVMTRLVLHELKNLTQYNWLLDGFPRTLPQAEALDRAY
  QIDTVINLNVPFEVIKQRLTARWIHPGSGRVYNIEFNPPKTMGIDDLTGE
  PLVQREDDRPETVVK............
   (Restrict the line length to 80 characters).


   You could send the file containing the sequence to: 
           service at bchs.uh.edu
The subject line must be:
   Subject: SSP
Example: mail -s SSP service at bchs.uh.edu < test.seq


Example of SSP output:		
*****************************
   ADENYLATE KINASE     
                    10        20        30        40        50
   pred A:    aaaaaaaaa          aaaaaaaaa     aaaaaaaaa     aaa
   AA         N  4.1  C          N  2.2  C     N  4.4  C     N  
   pred B:                  bbbb                                
   BB                       N2 C                                
   Predic     aaaaaaaaa     bbbb aaaaaaaaa     aaaaaaaaa     aaa
   a/acid     RLLRAIMGAPGSGKGTVSSRITKHFELKHLSSGDLLRDNMLRGTEIGVLA
                    60        70        80        90       100
   pred A:    aaaaaa       aaaaaaaaaaaaaaaaaaaaaaa     aaaaaaaaa
   AA         2.2  C       N    4.2    CN   2.4  C     N  5.4  C
   pred B:                 bbbbbbb                              
   BB                      N 2.6 C                              
   Predic     aaaaaa       aaaaaaaaaaaaaaaaaaaaaaa     aaaaaaaaa
   a/acid     KTFIDQGKLIPDDVMTRLVLHELKNLTQYNWLLDGFPRTLPQAEALDRAY

   The output of the prediction program presents not only final optimal
   variant of the secondary structure assign ment, but also a set of
   potential a-helix and b-strand segments that were computed without 
   consideration of their competition. Because the protein secondary 
   structure is finally stabilized during the formation of the tertiary 
   structure, the alternative variants of the a-helix and b-strand 
   segments may be important for methods of tertiary structure 
   prediction.

Reference:
  1.Solovyev V.V.,Salamov A.A.
  Method of calculation of discrete secondary structures 
  in globular proteins. Molek. Biol. 25:810-824,1991 (in Russ.)
  2.Solovyev V.V.,Salamov A.A. 1994,
  Secondary structure prediction based on  discriminant analysis. 
  In Computer analysis of Genetic macromolecules. (eds. Kolchanov N.A., Lim 
  H.A.), World Scientific, p.352-364.

Problems, comments, and suggestion:
   Can be mailed to solovyev at cmb.bcm.tmc.edu.
   





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