I'm trying to run Blaston, and still SIFT standalone. I am having database configuration problems, although I am getting the following:
arron @ arron-ideapad-z570 ~ / PhD / program / sift4.0.3b $ blast -core test / LACI. Fasta-db db / swissprot / BLAST database error: No nickname or index file found in the nucleotide database [db / swissprot /] search path [/ home / arron / phd / programs / sift4.0.3b :::]
After some advice from another thread, I have downloaded a protein database, for example SwissProot:
wget ftp://ftp.ebi.ac.uk/pub/databases/fastafiles/uniprot/uniprotkb_swissprot.gz zcat uniprotkb_swissprot.gz | Awk '{if (/ ^ & gt; /) {print> & gt; " $ 2} and {print $ _}} '& gt; Swissprot.fa
and then using MacBlueDebbed to create a blast database:
arron @ arron-ideapad-z570 ~ / pdf / programs / Sift4.0.3 b / db / swissprot $ makeblastdb -in swissprot.fa -dbtype prot Creating a new db, Current time: 10/27/2014 13:18:57 New db name: swissprot.fa New db Title: swissprot Fa sequence type: Keep the protein linkout: keep the MBT: T max file size: 1073741824B Adding the sequence from Fast; 54,643 pairs in sequence in 190039 seconds
However, I still get the same problem, am I doing wrong?
You listed the folder that is in the database file, not the database itself: / P>
blastn -query test / lacI.fasta -db db / swissprot / swissprot.fa
(Of course, this will not work either because you blast You are trying to use the protein database. You must use blastx)
Comments
Post a Comment