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
