Creating A Dna Sequence Database Locally For Blastplus

Question

[Eric Normandeau]

Hi,

I have a fasta file containing cDNA sequences and I would like to create a blastable database for blastplus, (using blastn) that I have installed locally. I am, however, unsuccessful up to now as I end up creating a PROTEIN database, although my file obviously contains DNA sequences. Here is the command I use, following blastplus user_manual.pdf:

makeblastdb -in my_file.fasta -title my_db -out ~/path/blastplus/database/my_db

And here is the output produced:

Building a new DB, current time: 07/26/2010 11:00:28
New DB name:   /path/blastplus/database/my_db
New DB title:  my_db
Sequence type: Protein
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1073741824B
Adding sequences from FASTA; added 1100 sequences in 0.0458999 seconds.

The user manual says that makeblastdb is supposed to recognise the data type automatically. Should it not recognize that I'm using DNA and not proteins?

Your suggestions are appreciated :)

Cheers

Answer 1

[Lars Juhl Jensen]

I think the option you are looking for is -dbtype nucl. I have seen auto-detection of protein vs. nucleotide sequences fail too many times for me to rely on it ;)

[Eric Normandeau]

That solved my problem quick :) I didn't see that option in the section on makeblastdb, they only list it in the Query section... Thanks!

Answer 2

[Haibao Tang]

If you are familiar with the old BLAST system, you can quickly convert old commands through the following script:

legacy_blast.pl formatdb -i t.fa -p F --print_only
/usr/bin/makeblastdb -dbtype nucl -in t.fa

The same command can convert blastall commands as well.

[Eric Normandeau]

Interesting :) although I only started to use blast with blastplus, but may be helpful to someone!