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
