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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" --------- See also -[SMC1afs mimotopes 07-01-2014d1643]
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