Blast searches

If you want to run a local blast search to find a specific protein or nucleotide you have to do the following:

Option A

Blast against a sequence

1. Get representatives sequences from the target feature that you are interested in
2. Blast against your sequence

blastn -query YOUR_QUERY -subject YOUR_SUBJECT -out OUTPUT -outfmt "6 qseqid sseqid slen qstart qend length mismatch gapopen gaps qseq"

Like this you will get the output without the alignment but with the sequence at the end.

Option B

1. Get representatives sequences from the target feature that you are interested in
2. Make a blast database with these representatives sequences. For that:

makeblastdb -dbtype nucl -in INPUT_DATA -parse_seqids -out OUTPUT_DATABASE

-dbtype refers to the kind of molecule (nucleotide or protein). There are several more flags that you can add. Check them in the manual.

3. Blast search

blastn -query YOUR_QUERY -db YOUR_DB -out OUTPUT