Local BLAST databases

So I installed a local database on my mac and BLASTed it for the first time, hurrah!

Commands are as follows:

To setup a local BLAST database:

makeblastdb -in (input FASTA sequences) -dbtype nucl -parse_seqids -hash_index -max_file_sz 1GB

Standard BLAST (after local DB is established–do not move DB files across folders or you will have to remake the local DB):

blastn -query (query seqs path) -task megablast -db (dabase path) -out (output path–empty txt file needs to be created already)

Useful tweak BLAST; gives you an alignment of all 10 sequences:

blastn -query (query seqs path) -task megablast -db (database path) -out (output path to empty txt file) -outfmt 3 -max_target_seqs 10

Advertisements

Leave a Reply

Fill in your details below or click an icon to log in:

WordPress.com Logo

You are commenting using your WordPress.com account. Log Out / Change )

Twitter picture

You are commenting using your Twitter account. Log Out / Change )

Facebook photo

You are commenting using your Facebook account. Log Out / Change )

Google+ photo

You are commenting using your Google+ account. Log Out / Change )

Connecting to %s

%d bloggers like this: