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GCG V. 9.0-GAP

Ellis Golub ellis at vesicle.dental.upenn.edu
Mon Jun 16 08:44:34 EST 1997


In article <m.mitchell-ya02408000R1206971358020001 at news.lif.icnet.uk>, m.mitchell at icrf.icnet.uk (Mike Mitchell) writes:
|> In article <338C4FCC.41C6 at gcg.com>, Irv Edelman <edelman at gcg.com> wrote:
|> 
|> > Francois JEANMOUGIN wrote:
|> > > 
|> > > [...Also posted to help at gcg.com...]
|> > > In article <5mfc74$66t at netnews.upenn.edu>,
|> > >         ellis at vesicle.dental.upenn.edu (Ellis Golub) writes:
|> > > [...]             .         .         .         .         .
|> > > >      151 AGNVRSYARMDIGTTHDDYANDVVARAQYYKQHGY............... 185
|> > > >                                           |
|> > > >        1 .................................GASARLLRAAIMGAPGS 17
|> > > >                                   .
|> > > [...]
|> > > 
|> > >         I saw such strange things using GCG9 gap, but had not time
|> > > to work around to see what's happen. I think there is a bug (big one)
|> > > in GCG9 gap. Also, that was with other sequences (but I can't
|> > > remember which ones!!!).
|> > >         Could Oxford Molecular (Ooooooops, sorry) GCG look around this
|> > > problem?
|> > 
|> > The two sequences being aligned here (sw:lyg_ansan and sw:kad3_bovin)
|> > share no significant similarity.
|> 
|> To add to what Irv said, try having a look at these two sequences with a
|> dotplot program and you'll see that these two seqs bear little relation to
|> each other.
|> 
|> -- 


Many people have commented on the lack of (biologic) relationship between 
the two test sequences, and suggested that the solution offered by gap v.9
is a correct representation of that fact.  I agree.  

However, one must always keep in mind what question is being asked.  If 
the question is: To what extent are these *sequences similar*, isn't 
the solution below more useful?

Ellis

 GAP of: lyg_ansan  check: 5420  from: 1  to: 185
 
ID   LYG_ANSAN      STANDARD;      PRT;   185 AA.
AC   P00718;
DT   21-JUL-1986 (REL. 01, CREATED)
DT   21-JUL-1986 (REL. 01, LAST SEQUENCE UPDATE)
DT   01-FEB-1996 (REL. 33, LAST ANNOTATION UPDATE)
DE   LYSOZYME G (EC 3.2.1.17) (1,4-BETA-N-ACETYLMURAMIDASE) (GOOSE-TYPE . . . 
 
 to: kad3_bovin  check: 1291  from: 1  to: 226
 
ID   KAD3_BOVIN     STANDARD;      PRT;   226 AA.
AC   P08760;
DT   01-NOV-1988 (REL. 09, CREATED)
DT   01-APR-1990 (REL. 14, LAST SEQUENCE UPDATE)
DT   01-NOV-1995 (REL. 32, LAST ANNOTATION UPDATE)
DE   GTP:AMP PHOSPHOTRANSFERASE MITOCHONDRIAL (EC 2.7.4.10) (AK3). . . . 

 Symbol comparison table: /disk6/people/gcg90/gcgcore/data/moredata/oldpep.cmp
 CompCheck: 2543

         Gap Weight:      5      Average Match:  5.402
      Length Weight:      3   Average Mismatch: -3.964

            Quality:    829             Length:    244
              Ratio:  4.481               Gaps:     35
 Percent Similarity: 64.072   Percent Identity: 31.737

        Match display thresholds for the alignment(s):
                    | = IDENTITY
                    : =   4
                    . =   1

 lyg_ansan x kad3_bovin    May 26, 1997 20:58  ..

                  .         .         .         .         .
       1 .......RTDCYGNVNRIDTTGASCKTAKP.EGLSYCGVSASKKIAERD. 41
                |:.. |..:. .:| .|::.:|. | |..  :| | .:  || 
       1 GASARLLRAAIMGAPGSGKGT.VSSRITKHFE.LKH..LS.SGDLL.RDN 44
                  .         .         .         .         .
      42 .LQA..MDRY.KTIIKKVGEKLCVEPAVIAGIISRESHAGKVLKN..GWG 85
          |::  :: . ||:|.: | || :...|:: :: :|      |||  .: 
      45 MLRGTEIGVLAKTFIDQ.G.KL.IPDDVMTRLVLHE......LKNLTQY. 84
                  .         .         .         .         .
      86 DR.GNGF..GLMQVD..KRSHKPQG..TWNG..EV...HIT.....QGTT 118
         ::  :||  :| |.:  .|:.: ::  .:|.  ||   ::|     .|.:
      85 NWLLDGFPRTLPQAEALDRAYQIDTVINLNVPFEVIKQRLTARWIHPGSG 134
                  .         .         .         .         .
     119 .IL.INF..IKT..IQ....KKFPSWTKDQQ...LKGGISAYNAGAGNVR 155
          :. |:|   ||  |:    ..:. :..|:.   :|  :.||:|.:: | 
     135 RVYNIEFNPPKTMGIDDLTGEPLVQREDDRPETVVK.RLKAYEAQTEPVL 183
                  .         .         .         .    
     156 SYAR....MD.I.GT.THDDYANDVVARAQY.YKQHGY...... 185
         .| |    :: : || |:. ::: | |  |  ..|::       
     184 EYYRKKGVLETFSGTETNKIWPH.VYAFLQTKLPQRSQETSVTP 226


--
Ellis Golub                  Phone: (215) 898-4629
Biochemistry Department      FAX:   (215) 898-3695
University of Pennsylvania   ellis at biochem.dental.upenn.edu
School of Dental Medicine             
4001 Spruce Street
Philadelphia, PA 19104-6003



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