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GCG V. 9.0-GAP

Ellis Golub ellis at vesicle.dental.upenn.edu
Fri Jun 20 08:52:32 EST 1997


In article <33A78399.167E at cc.huji.ac.il>, Iddo Friedberg <idoerg at cc.huji.ac.il> writes:
> 
|> I ran GAP using the same matrix and gap penalties as Ellis, only I added
|> a check vs. 100 randomizations:
|> 
|> ** Average quality based on 100 randomizations: 853.6 +/- 31.6 **
|> 
|> GAP's quality score is 829, rather close to a random mean of 853 with a
|> standard deviation of 31.6 
|> 
|> Therefore, I don't think there is any significance, biological OR
|> statistical to the result provided in this case by GAP. GAP _always_
|> finds something...
|> 
|> Iddo
|> 
|> >  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
|> > 
|> 
|> 

Your point is well taken.  I reiterate mine however.  If I want 
to know *how these (admittededly unrelated) sequences best align,* the
output using matr=oldpep tells me, while the output using the default does not.

Ellis







--
Ellis Golub                  Phone: (215) 898-4629
Biochemistry Department      FAX:   (215) 898-3695
University of Pennsylvania   ellis at biochem.dental.upenn.edu
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