Hello all!
I've been using blat this year quite a lot, with very good results
for proteome comparison, but I recenly found a weard case with two
proteins which are quite similar (I paste the aligment below) and blat
returns an empty file (just the field descriptions) like they were
completely different.
Is this result I reproduce here normal? I found it weard beacuse there
is a fragment of 7 AA which are identical and with the "-tileSize=5"
option (default) I got no results but with "-tileSize=4" I find a match.
Thank you very much and congratulations for your program, much more easy
to use, port and install than NCBI blast
Suporting information:
my two proteins are (expresed in UNIPROT codes):
P0C054
Q9HZ98
my blat version:
blat - Standalone BLAT v. 34 fast sequence search command line tool
(linux x86_32)
executed command:
blat -prot Q9HZ98.UP.fasta P0C054.UP.fasta
P0C054+Q9HZ98.blatdefaults.psl
aligment of those two proteins with clustalw:
CLUSTAL 2.0.10 multiple sequence alignment
sp|P0C054|IBPA_ECOLI
MRN-FDLSPLYRSAIGFDRLFNHLENNQSQSNGG-YPPYNVELVDENHYR
tr|Q9HZ98|Q9HZ98_PSEAE
MSNAFSLAPLFRHSVGFDRFNDLFESALRNEAGSTYPPYNVEKHGDDEYR
* * *.*:**:* ::****: : :*. :. *. *******
.::.**
sp|P0C054|IBPA_ECOLI
IAIAVAGFAESELEITAQDNLLVVKGAHADEQKE-RTYLYQGIAERNFER
tr|Q9HZ98|Q9HZ98_PSEAE
IVIAAAGFQEEDLDLQVERGVLTVSGGKREKSTDNVTYLHQGIAQRAFKL
*.**.*** *.:*:: .: .:*.*.*.: ::..:
***:****:* *:
sp|P0C054|IBPA_ECOLI
KFQLAENIHVRGANLVNGLLYIDLERVIPEAKKPRRIEIN---------
tr|Q9HZ98|Q9HZ98_PSEAE
SFRLADHIEVKAASLANGLLNIDLVRLVPEEAKPKRIAINGQRPALDNQ
.*:**::*.*:.*.*.**** *** *::** **:** **
--
Oscar Conchillo Solé
Group of Computational Biology and Proteomics
IBB Data Center Manager and Linux Sysadmin
Institut de Biotecnologia I Biomedicina (UAB)
mail: [email protected]
telf: 0034 93581 4431; 0034 93586 8939
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