How To Blast A Sequence Against Multiple Databases

Question: How To Blast A Sequence Against Multiple Databases

7.3 years ago by

Manju • 40

Manju • 40 wrote:

Hello,

I have downloaded all the chromosome of Bos taurus and I have changed them in blast format using makeblastdb..and now I want to locally blast my sequence against these all chromosomes. now I have 29 databases. Is there any method by which I am able to blast my sequence against all 29 databases in my program.

What should I write in database????

@params = ('database' => '????????', 'outfile' => 'blast2.out', '_READMETHOD' => 'Blast', 'prog'=> 'blastn');

Thanks Manju Rawat

blast • 9.7k views

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modified 11 weeks ago by Biostar ♦♦ 20 • written 7.3 years ago by Manju • 40

7.3 years ago by

Digiomics • 160

Netherlands

Digiomics • 160 wrote:

You could also use the blastdb_aliastool included in the NCBI blast package to aggregate your BLAST databases to a single virtual database.

ADD COMMENT • link written 7.3 years ago by Digiomics • 160

7.1 years ago by

Torst • 900

Australia

Torst • 900 wrote:

There is no need to create custom single databases (real or alias).

I'm pretty sure the BLAST "-d" and BLAST+ "-db" accept SPACE-SEPARATED multiple databases on the one command line. You just have to ensure you quote them in your shell, or within a Perl string. eg.

blastall -p blastp -d "nr sprot trembl" -i q.fa

ADD COMMENT • link written 7.1 years ago by Torst • 900

7.3 years ago by

Chris • 1.6k

Munich

Chris • 1.6k wrote:

Why not creating a single database by merging the chromosomes into one big fasta file and then formatting it?

Not sure what you mean by this: @params = ('database' => '????????', 'outfile' => 'blast2.out', '_READMETHOD' => 'Blast', 'prog'=> 'blastn');

ADD COMMENT • link written 7.3 years ago by Chris • 1.6k

This answer is bad. Why is everyone upvoting it? That is so much more work and may not even be possible in some cases to do.

ADD REPLY • link written 5.0 years ago by axa9070 • 20

I don't see how this approach is either bad or much more work. The objective of the OP is to have a single database. Chris proposes to merge the fasta files and create one database while you suggest to combine existing databases. In this case, the OP had access to the original fasta files, which a simple 'cat' command would have joined and then he could have used a command he already knew about and had used to create his databases. Clearly, both solutions seem workable. Your solution also happens to be the second most upvoted solution, which has been there for over two years. It seems to me that there is no need to call any answer bad and to question the judgement of multiple users over the course of 2.3 years. Even less on the first day you joined this forum ;)

ADD REPLY • link modified 5.0 years ago • written 5.0 years ago by Eric Normandeau ♦ 10k

The answer is bad. The user asked how to blast against 29 databases. "Is there any method by which I am able to blast my sequence against all 29 databases in my program?"

The answer "go compile a new database" is an indirect work around to the problem. It may even be good advice in this particular instance - but it did not answer the question asked.

Why don't I want to do that? Because it's moronic to create multiple permutations of databases when I already have them compiled. This means my usage of disk space balloons every time I do a search. Not to mention it is annoying and time consuming.

I came here with the exact same question. Thankfully there are several good options provided by others below.

ADD REPLY • link modified 3.9 years ago • written 3.9 years ago by jeremy.cox.2 • 90

It looks suspiciously like he's trying to run blast via a perl script.

ADD REPLY • link written 7.3 years ago by Razzmataz • 30

Ah, right, now I remember. The '@'-construct is a hint... Well, since I'm in Python I do not come across such things very often. ;)

ADD REPLY • link written 7.3 years ago by Chris • 190

7.1 years ago by

Manu Prestat ♦ 3.9k

Marseille, France

Manu Prestat ♦ 3.9k wrote:

You can do your alias easily by yourself:

example:

cd myblastdbs/
gedit myOwnblastDB.nal

then follow this (an example is the genbank nt.nal file):

#
# myOwnblastDB.nal is an alias file for all my chromosomes
#
#
TITLE all my chromosomes
#
DBLIST chr1 chr2 chr3 chr4 chri chr24
#
#GILIST
#
#OIDLIST
#

It is very simple, and works very fine!

ADD COMMENT • link written 7.1 years ago by Manu Prestat ♦ 3.9k

5.0 years ago by

axa9070 • 20

axa9070 • 20 wrote:

http://www.ncbi.nlm.nih.gov/books/NBK1763/#CmdLineAppsManual.Aggregate_existing_BLA

To combine the two nematode nucleotide databases, named “nematode_mrna” and “nematode_genomic", we use the following command line:

$ blastdb_aliastool -dblist "nematode_mrna nematode_genomic" -dbtype nucl \ -out nematode_all -title "Nematode RefSeq mRNA + Genomic"

ADD COMMENT • link written 5.0 years ago by axa9070 • 20

7.3 years ago by

Eric Normandeau ♦ 10k

Quebec, Canada

Eric Normandeau ♦ 10k wrote:

If you place your 29 chromosomes in the same fasta file, you should be able to create your single database using the makeblastdb program. Just use blastn then to blast on the database containing all your chromosomes.

ADD COMMENT • link written 7.3 years ago by Eric Normandeau ♦ 10k

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