BLAST+ basic help

[Tapi]

Hi,

i am new here so first of all I would like to say Hi to everybody. This forum is really useful



My problem is that I got a genome assembly consisting in a multifasta file of scaffolds.

I wanted to use BLAST+ to transform it to a database and later use a gene sequence from a closely related species which is alreeady sequenced to recover scaffolds with the homologous gene.

So I use my multiFASTA file and execute:

makeblastdb -in database.scf.fasta -parse_seqids -dbtype nucl

And got:

Building a new DB, current time: 06/19/2013 18:16:55
New DB name: database.scf.fasta
New DB title: database.scf.fasta
Sequence type: Nucleotide
Keep Linkouts: T
Keep MBits: T
Maximum file size: 1000000000B
Adding sequences from FASTA; added 173006 sequences in 57.8037 seconds.




And now run blast to look for a sequence in FASTA format (gene.fasta) in the database (database.scf.fasta):

blastn -db database.scf.fasta -query gene.fasta -out result



But I got no results, which is impossible.

I would really appreciate some basic help in this

Best

[mastal]

BLAST+ basic help

Try using the sequence of one (or part of one) of the scaffolds in your database as the query,
since that should give a 100% identity match to your database, and see what result you get.

[GenoMax]

I am not sure what happens if you do not provide a name for your blast index file when you are building it (e.g. -out db_name). Did you get the "database.scf.fasta".nin/.nhr etc files after the index build completed?

[cliffbeall]

You might try tblastx, depending on how closely related the bacteria are. I am studying two species from the same genus and similarities are easily detectable in the translated proteins but are mostly below the noise threshold at nucleotide level.