IUBio Biosequences .. Software .. Molbio soft .. Network News .. FTP

searching profiles in PROSITE

Othmar Pfannes wopf at chbs.CIBA.COM
Thu Apr 27 10:21:53 EST 1995


 
 Dear Netters,
 
 I would appreciate any help re the following problem :
 
 The PROSITE database seems to contain 2 kinds of "Motif" entries:
 a) patterns like ....ABCDEFG..
 b) profiles in terms of  matrices   
 
 It seems like I can use the GCG program "motifs" to identify
 patterns within PROSITE that are contained in my sequence.
 But "motifs" seems to neglect PROSITE info presented as matrices.
 
 Correct?
 
 If yes, then which GCG program allows me to identify motifs that are
 represented as matrices  within PROSITE?
 
 If there is none, are there other programs available? 
 
 Remark:
 It seems like that the GCG program "profilescan" does not do the job . 
 It only checks a
 "validated" profile data file that also contains info like gap penalties
 and parameters for normalizing scores and which is not included in
 PROSITE.
 
 Thanks for your help
 
 Othmar
 --
 ====================================================================  
                                    ||                              ||
     Dr. Othmar Pfannes             ||                              ||
          CIBA                      || Vox: + 41 + 61 + 697 8685    ||
   IS/Scientific Services           ||                              ||
     R-1008.Z2.22                   || Fax: + 41 + 61 + 697 8973    ||
     CH-4002 Basel                  ||                              ||
      Switzerland                   || Internet: wopf at chbs.CIBA.COM ||
                                    ||                              ||
 =====================================================================
 
> 
> 
> 


--
====================================================================  
                                   ||                              ||
    Dr. Othmar Pfannes             ||                              ||
         CIBA                      || Vox: + 41 + 61 + 697 8685    ||
  IS/Scientific Services           ||                              ||
    R-1008.Z2.22                   || Fax: + 41 + 61 + 697 8973    ||
    CH-4002 Basel                  ||                              ||
     Switzerland                   || Internet: wopf at chbs.CIBA.COM ||
                                   ||                              ||
=====================================================================



More information about the Info-gcg mailing list

Send comments to us at biosci-help [At] net.bio.net