makeblastdb fail!

[Brie423]

Hi!

I'm brand new at this, and I have been trying to use the makeblastdb command on TACC (tried both lonestar and stampede). I have the blast modules loaded. I have downloaded the protein sequences from the genomes of several animals from the NCBI ftp site and eventually would like to blast my de novo transcriptome against the protein databases for annotation purposes.

I have used the makeblastdb command before with no problems, but for the past two days I've been stumped because it is not giving me the correct output files even when i rerun a makeblastdb command that was previously successful.

my command line looks like this:
$ makeblastdb -in protein.fa -dbtype prot -out Fugu.prot.db

instead of getting a Fugu.prot.db output file, i'm getting three binary files:
Fugu.prot.db.phr
Fugu.prot.db.pin
Fugu.prot.db.psq

any ideas on what to try next?

Thanks!!!!

[GenoMax]

It is not the makeblastdb that is failing ...

A blast database consists of files of the kind you list above (http://www.ncbi.nlm.nih.gov/books/NBK1763/). You are only specifying a "prefix" name for the database files when you specify -out Fugu.prot.db (the blast index files will have names prefix.phr, prefix.pin, prefix.psq).

"Prefix" is the name you will use for your database when you actually run the blast searches.

$ blastp -query sequence.fa -db Fugu.prot.db -out outfile

[Brie423]

so for instance when I do a blastx after the makeblastdb I should do something like this:

blastx -outfmt 7 -db path/Fugu.prot.db -max_target_seqs 1 -query path/Wrasse.transcriptome -out Fugu_wrasse.blastx.txt

or something like this:

blastx -outfmt 7 -db path/Fugu.prot.db* -max_target_seqs 1 -query path/Wrasse.transcriptome -out Fugu_wrasse.blastx.txt


Thanks! as I said I'm really new at this. I really appreciate your help!

[GenoMax]

For ref: blastx application translates a nucleotide query and searches it against protein subject sequences or a protein database.

So long as "Wrasse.transcriptome" contains DNA sequence you are good to go.