Question: blastdbcmd vs blastdb_aliastool for custom database
0
gravatar for blanca
2.5 years ago by
blanca10
Spain
blanca10 wrote:

From my understanding, both tools blastdbcmd and blastdb_aliastool would allow the user to subset a database from GI numbers of a bunch of sequences using them as follows:

> blastdbcmd -db nr -entry_batch human.gi -target_only -out human.txt
> blastdb_aliastool -gilist human.gi -db nr -out nr_human

Apart from one of them giving as result a file with sequences and the other one an already formatted database, is there any other difference? Speed/performance, maybe?

Could the output of blast_aliastool command be used alone or would it need the rest of the nr database to be uncompressed for it to work? In the latest case, the first way of producing a subset of a database -although involving an extra step of making the database again from the sequences- will be preferably if the disk space is limited.

blast • 1.1k views
ADD COMMENTlink written 2.5 years ago by blanca10
0
gravatar for genomax
2.5 years ago by
genomax67k
United States
genomax67k wrote:

Since the gi numbers have gone away blastdb_aliastool is not going to work. I don't see an option to use accession numbers with aliastool in the latest blast+ package.

ADD COMMENTlink modified 2.5 years ago • written 2.5 years ago by genomax67k
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