BLAST of SMC1afs mimotopes against human unusual peptide database 07-01-2014d1640

2014-08-29

BLAST of SMC1afs mimotopes against human unusual peptide database 07-01-2014d1640

made a blast database
by navigating to C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-01-2014d1325\frameshift databases 07-01-2014d1424\Human Unusual Peptide BLAST Database
and then
makeblastdb -in Human_Unusual_Peptide_Database.fa -dbtype prot -title protdb -out human_unusual_peptide_database

blastp -task blastp-short -db "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-01-2014d1325\frameshift databases 07-01-2014d1424\Human Unusual Peptide BLAST Database\human_unusual_peptide_database" -query "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-01-2014d1325\SMC1afs mimotopes\smc1afs_mimotopes.fasta" -out "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-01-2014d1325\SMC1afs blast against human unusual peptides\blast results 07-01-2014d1645.txt"
^I'm getting errors with this command,and I'm not sure how to fix it.

performing a blast against a database only seems to work if the command line has navigated to the directory with the database

I'll try navigating to the directory and calling the command again
directory: "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-01-2014d1325\frameshift databases 07-01-2014d1424\Human Unusual Peptide BLAST Database"
blastp -task blastp-short -db human_unusual_peptide_database -query smc1afs_mimotopes.fasta -out test.txt
^this works

What if I set a windows environment variable for BLASTDB and put the database where I specified?
Can I call:
blastp -task blastp-short -db human_unusual_peptide_database -query "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-01-2014d1325\SMC1afs mimotopes\smc1afs_mimotopes.fasta" -out "C:\Users\kurtw_000\Documents\kurt\storage\CIM Research Folder\DR\2014\07-01-2014d1325\SMC1afs blast against human unusual peptides\blast results 07-01-2014d1645.txt"