Formatdb For Chromosome Database?

Question

[User 4143]

Hi,

I recently downloaded the new Fugu v5 assembly database from IMCB (http://www.fugu-sg.org/downloads/downloads3.htm). This is my first time using a chromosome level database (I am used to contig and scaffold).

I tried to use formatdb as I normally would to get the output files; however, nothing seems to be happening. Is there a way to use formatdb to format chromosome databases or am I supposed to do it in a different way? Am I missing some steps that precede formatdb?

[Pierre Lindenbaum]

what is the size of the fasta ? what are your parameters for formatdb ?

[Daniel Standage]

And what is written to the formatdb.log file?

Answer 1

[Simon Cockell]

OK, I downloaded this file and used formatdb from the BLAST 2.2.25 package on OS X.

$ gunzip fugu5_chromosomes.fa.gz
$ formatdb -o T -p F -i fug5_chromosomes.fa
$ blastall -p blastn -d fugu5_chromosomes.fa -i testseq.fa

Works just fine for me. Without any more specific information it is really hard to debug your specific problem. I've packaged the output of formatdb and you can download it from here (94MB).

(for the record, the contents of formatdb.log:

========================[ Apr 1, 2011  2:34 PM ]========================
Version 2.2.25 [Feb-01-2011]
Started database file "fugu5_chromosomes.fa"
Formatted 45 sequences in volume 0
SUCCESS: formatted database fugu5_chromosomes.fa

).