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
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
Comment