[BiO BB] confusion about the psi-blast profile

[jiye at eden.rutgers.edu]

hi, 

I'm a graduate student at Rutgers Univ. NJ, USA. I'm seeking 
some kind help on a question I have recently regarding to the 
profile from psi-blast. 

I use the standlone blast program and run the blastpgp for 3 
iterations and then the makemat to get the position specific
scoring matrix. The commands I use are like

blastpgp -d protein/nr -i test.seq -o test.rst -j 3 -C test.chk
makemat -P test -d protein/nr

And I put the following sequence in the test.seq, the nr protein
database is downloaded from the ncbi web site. 

> S0_Sinorhizobium meliloti aa_pep18
mggfidiqapleqegtkavvrnwlrkigdpvksgdplveletdkvtqevs
apadgvlaeilmrngddatpgavlgrigseaagaghaphyspavrhaaee
ygldpatvtgtgrggrvtradmdraftarqegpasvaaeagdrgaapksr
riphsgmraaiaehmlnsvttaphvtavfeadfsavmrhrdehgkrlaad
gtklsytayvvsacvaamravpevnsrwhedaletfddinigvgislgdk
glvvpvihraqdlslaeiaarlqdlttrarsnalsradvtggtftisnhg
asgsllaapiiinqpqsailgvgkldkrvivrevdgadtiqirpmayvsl
tidhraldghqtnawlthfvrvietwpk

The result score I read back from the test.mtx is like: 

-32768  -291  -32768  -341  -521  -407  -185  -480  -359  -64  -338  
80  980  -425  -457  -238  -338  -351  -261  -113  -343  -100  -296  -
32768  -32768  -397  

-32768  153  -32768  -361  -298  -178  -500  423  -364  -495  -291  -
502  -408  -216  -352  -288  -360  477  -70  -412  -504  -100  -448  -
32768  -32768  -397  
.....
.....

Since I have no experience with psi-blast before, I'm not very sure
it's right or not. But I feel that something is wrong. The minimum
number -32678 is repeatedly appears at all position of column 1, 3, 
19, and 20. And other numbers also look either too small or too large. 
However, I couldn't find where is the problem. I also tried the database
of swissprot, the result is similar. It's really appreciated if someone
can tell me whether there is anything wrong with such kind of result. 

Best regards, 

-Jiankuan