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GCG V. 9.0-GAP

Iddo Friedberg idoerg at cc.huji.ac.il
Wed Jun 18 01:43:37 EST 1997


Ellis Golub wrote:
> 


> 
> 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
> 

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
> 


--

Iddo Friedberg                             
Phone: (972)-2-6758647                      
email: idoerg at cc.huji.ac.il                
web: http://www.ls.huji.ac.il/~idoerg     
More info: finger idoerg at cc.huji.ac.il



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