[rhinoceros]

This might work:

makeblastdb -in $(cat Strains/*.fasta) -dbtype 'nucl' -out db/stec_samples

[maubp]

I am wondering if you could tell me how I can make a database from different files in batch?

BLAST does not like this kind of command, where the second FASTA file is considered to be a positional argument:

makeblastdb -in Strains/example1.fasta Strains/example2.fasta -dbtype nucl -out db/stec_samples

From past experimentation, I know it will work if you quote the list of filenames making them space separated (filenames with spaces are a problem):

makeblastdb -in "Strains/example1.fasta Strains/example2.fasta" -dbtype nucl -out db/stec_samples

[poudap]

Unfortunately the $(cat Strains/*.fasta) command did not work.

The command space seperated also gave error:
BLAST options error: File Sample_no2.fasta does not exist.

[maubp]

The simple brute force solution is make a single merged FASTA file (e.g. using the cat command), and then build a BLAST database out of that.

[kaps]

Dear all, In creating a local blast database, I downloaded fasta files from ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/ and http://www.ncbi.nlm.nih.gov/sites/nu...=%22Viruses%22[PORG]+AND+srcdb_refseq[PROP]. The former appeared larger than the latter, which of them is better? Do both both contain nr sequences? are they different?

Thanks

[maubp]

Dear all, In creating a local blast database, I downloaded fasta files from ftp://ftp.ncbi.nlm.nih.gov/refseq/release/viral/ and http://www.ncbi.nlm.nih.gov/sites/nu...=%22Viruses%22[PORG]+AND+srcdb_refseq[PROP]. The former appeared larger than the latter, which of them is better? Do both both contain nr sequences? are they different?

Thanks

I think a separate thread would be a good idea for this question. See also http://blastedbio.blogspot.co.uk/201...-chimeras.html and http://www.ncbi.nlm.nih.gov/pubmed/?term=25428358

[kaps]

I think a separate thread would be a good idea for this question. See also http://blastedbio.blogspot.co.uk/201...-chimeras.html and http://www.ncbi.nlm.nih.gov/pubmed/?term=25428358

Hello Maubp,

Thanks for the blog links. i have also created a seperate thread as advised. its now called fasta files from NCBI

[maubp]

See http://seqanswers.com/forums/showthread.php?t=50017 for kaps's thread.