PSI-BLAST: no hits in 1st iteration

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Mon Jun 5 11:13:23 EST 2000


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







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