I am trying to run blastn, and then also SIFT standalone. I am having database configuration issues however as I am getting the following:
arron@arron-Ideapad-Z570 ~/Phd/programs/sift4.0.3b $ blastn -query test/lacI.fasta -db db/swissprot/ BLAST Database error: No alias or index file found for nucleotide database [db/swissprot/] in search path [/home/arron/Phd/programs/sift4.0.3b:::] After some advice from other threads, I downloaded a protein database, for example swissprot:
wget ftp:// zcat uniprotkb_swissprot.gz | awk '{if (/^>/) { print ">" $2} else { print $_}}' > swissprot.fa and then used makeblastdb to create a blast database:
arron@arron-Ideapad-Z570 ~/Phd/programs/sift4.0.3b/db/swissprot $ makeblastdb -in swissprot.fa -dbtype prot Building a new DB, current time: 10/27/2014 13:18:57 New DB name: swissprot.fa New DB title: swissprot.fa Sequence type: Protein Keep Linkouts: T Keep MBits: T Maximum file size: 1073741824B Adding sequences from FASTA; added 546439 sequences in 19.0039 seconds. yet I am still getting the same problem. What am I doing wrong?
2 Answers
You've listed the folder that the database file is in, not the database itself. Try:
blastn -query test/lacI.fasta -db db/swissprot/swissprot.fa (of course, that won't work either because you'r trying to use a protein database for blastn. You'd need to use blastx)
You could try running protein blast, because swissprot is a protein database, and blastn is for nucleotide sequences
