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
