question about command-line PSI-BLAST

Martin S geneman at stanford.edu
Mon Jun 9 03:56:17 EST 2003


I'm hoping you might have a minute to answer a problem I have with 
running psi-blast from command line.  I am using BLASTP 2.2.6 running on 
a Windows XP installed on an Intel machine

I am having trouble running  blastpgp.exe from command line.  This is 
what I type:

..\blastpgp -i seq1.fasta -B align1.aln -j 1 -d somedatabase.fasta

And I get:

[NULL_Caption] WARNING:
Invalid character or wrong number of characters in sequence index 30
[NULL_Caption] WARNING:
None of the alignment sequences equals the query sequence
[NULL_Caption] WARNING:
Cannot recover alignment checkpoint

The files are as I found in the documentation provided:

seq1.fasta:

 >26SPS9_Hs
IHAAEEKDWKTAYSYFYEAFEGYDSIDSPKAITSLKYMLLCKI
LKCVAQASKNRSLADFEKALTDYRAELRDDPIISTHLAKLYDN
SKADVERKLSQMILDKKFHGILDQGEGVLIIFDEPP

align1.aln:

26SPS9_Hs     IHAAEEKDWKTAYSYFYEAFEGYdsidspkaits
F57B9_Ce      LHAADEKDFKTAFSYFYEAFEGYdsvdekvsalt
YDL097c_Sc    ILHCEDKDYKTAFSYFFESFESYhnltthnsyek
YMJ5_Ce       LYSAEERDYKTSFSYFYEAFEGFasigdkinats
FUS6_ARATH    KNYIRTRDYCTTTKHIIHMCMNAilvsiemgqft
COS41.8_Ci    SLDYKLKTYLTIARLYLEDEDPVqaemyinrasl
644879        KCYSRARDYCTSAKHVINMCLNVikvsvylqnws
YPR108w_Sc    IHCLAVRNFKEAAKLLVDSLATFtsieltsyesi
eif-3p110_Hs  SKAMKMGDWKTCHSFIINEKMNGkvw--------
T23D8.4_Ce    SKAMLNGDWKKCQDYIVNDKMNQkvw--------
YD95_Sp       IYLMSIRNFSGAADLLLDCMSTFsstellpyydv
KIAA0107_Hs   LYCVAIRDFKQAAELFLDTVSTFtsyelmdyktf
F49C12.8_Hs   LYRMSVRDFAGAADLFLEAVPTFgsyelmtyenl
Int-6_Mm      KFQYECGNYSGAAEYLYFFRVLVpatdrnalssl

26SPS9_Hs     SLADFEKALTDY----------------------
F57B9_Ce      rslkdfqvafgsf---------------------
YDL097c_Sc    aynnrslldfntalkqy-----------------
YMJ5_Ce       krslkdfvkalaeh--------------------
FUS6_ARATH    vnpelgnsyneviapqdiatygglcalasfdrse
COS41.8_Ci    eqtkalekalncailapagqqrsrmlatlfkder
644879        kqaakclllasfdhcdfpellspsnvaiygglca
YPR108w_Sc    yasdyasyfpyllety------------------
eif-3p110_Hs  ----------------------------------
T23D8.4_Ce    ----------------------------------
YD95_Sp       ylcdysgffrtladve------------------
KIAA0107_Hs   rysvffqslavv----------------------
F49C12.8_Hs   esyydchydrffiqlaale---------------
Int-6_Mm      wslfvffnhpkgrdniidlflyqpqylnaiqtmc

26SPS9_Hs     ----RAELRDDPIISTHLAKLYDNLLEQNLIRVI
F57B9_Ce      ----PQELQMDPVVRKHFHSLSERMLEKDLCRII
YDL097c_Sc    ----EKELMGDELTRSHFNALYDTLLESNLCKII
YMJ5_Ce       ----KIELVEDKVVAVHSQNLERNMLEKEISRVI
FUS6_ARATH    ----KSNLLLDIHLHDHVDTLYDQIRKKALIQYT
COS41.8_Ci    ----QLMPHQKAITADGSNILHRAVTEHNLLSAS
644879        ----KDNLLLDMYLAPHVRTLYTQIRNRALIQYF
YPR108w_Sc    ----ANVLIPCKYLNRHADFFVREMRRKVYAQLL
eif-3p110_Hs  ----DLFPEADKVRTMLVRKIQEESLRTYLFTYS
T23D8.4_Ce    ----NLFHNAETVKGMVVRRIQEESLRTYLLTYS
YD95_Sp       ----VNHLKCDQFLVAHYRYYVREMRRRAYAQLL
KIAA0107_Hs   ----EQEMKKDWLFAPHYRYYVREMRIHAYSQLL
F49C12.8_Hs   ----SERFKFDRYLSPHFNYYSRGMRHRAYEQFL
Int-6_Mm      lrecESVLVNDFFLVACLEDFIENARLFIFETFC

Besides getting psiblast to work, I'm also wondering if there is there a 
way to get the PSSM files obtained from semi-automated PSI-BLAST (on the 
ncbi servers) to work on command-line PSI-BLAST

Regards,
Martin S





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