This message has been posted by: Arne Mueller <a.mueller at REMOVE-THIS-TO-SENDicrf.icnet.uk>
Hi All,
I came across a strange problem when running psi-blast: it didn't find
any hits in the first iteration (which is the normal gap-Blast step) but
then still goes into iteration 2 and finds itself. Do you have any
explanation for this?
here's my commandline:
query is:
>90740
MDSAKxxxxxxxxxxxxxxxxxxxxxGTDCIVDxxxxxxxxxxxxxxxxxxxxQD
[ off course it's stupid to psi-blast that kind of query - but still it
doens't explain the observed behaviour, does it? ]
blastpgp -i 90740.seq -d my_db -j 5 -h 0.0005 -e 100.0 -v 0 -b 2000 >
90740.blast
and here's the output (the query is part of the protein database I
used):
BLASTP 2.0.12 [Apr-21-2000]
Reference: Altschul, Stephen F., Thomas L. Madden, Alejandro A.
Schaffer,
Jinghui Zhang, Zheng Zhang, Webb Miller, and David J. Lipman (1997),
"Gapped BLAST and PSI-BLAST: a new generation of protein database search
programs", Nucleic Acids Res. 25:3389-3402.
Query= 90740
(55 letters)
Database: /bmm/data/blast/20000509/nrbagpuss
576,299 sequences; 168,862,208 total letters
Searching..................................................done
***** No hits found ******
Searching..................................................done
Results from round 2
CONVERGED!
>90740 query,ref,sp,pir,gb,emb
Length = 55
Score = 26.8 bits (55), Expect = 27
Identities = 14/55 (25%), Positives = 14/55 (25%)
Query: 1 MDSAKXXXXXXXXXXXXXXXXXXXXXGTDCIVDXXXXXXXXXXXXXXXXXXXXQD 55
MDSAK GTDCIVD QD
Sbjct: 1 MDSAKIINIILSLFLPPVAVFLARGWGTDCIVDIILTILAWFPGMLYALYIVLQD 55
Database: /bmm/data/blast/20000509/nrbagpuss
Posted date: Jun 2, 2000 7:42 PM
Number of letters in database: 168,862,208
Number of sequences in database: 576,299
Lambda K H
0.301 0.0691 0.162
Lambda K H
0.270 0.0242 0.230
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Hits to DB: 3318962
Number of Sequences: 576299
Number of extensions: 11215
Number of successful extensions: 1
Number of sequences better than 100.0: 1
Number of HSP's better than 100.0 without gapping: 1
Number of HSP's successfully gapped in prelim test: 0
Number of HSP's that attempted gapping in prelim test: 0
Number of HSP's gapped (non-prelim): 1
length of query: 55
length of database: 168,862,208
effective HSP length: 34
effective length of query: 21
effective length of database: 149,268,042
effective search space: 3134628882
effective search space used: 3134628882
T: 11
A: 40
X1: 16 ( 6.9 bits)
X2: 38 (14.8 bits)
X3: 64 (24.9 bits)
S1: 42 (22.1 bits)
S2: 51 (25.2 bits)
thanks a lot for comments ;-)
Arne
--
Arne Mueller
Biomolecular Modelling Laboratory
Imperial Cancer Research Fund
44 Lincoln's Inn Fields
London WC2A 3PX, U.K.
phone : +44-(0)207 2693405 | fax :+44-(0)207-269-3534
email : a.mueller at icrf.icnet.uk | http://www.bmm.icnet.uk
