Hi Makis,

Comments below... I have CC'd the galaxy-dev mailing list.

2012/3/29 Makis Ladoukakis <makis4e...@hotmail.com>:
> Dear Peter,
> I am trying to send an e-mail inquiry in galaxy-dev mailing list but I keep
> getting this error and my  e-mail bounces back. Can you help me out please?
> Thank you in advance,
> Makis Ladoukakis

Have you also tried emailing galaxy-dev@lists.bx.psu.edu directly?
You wouldn't normally use galaxy-dev-requ...@lists.bx.psu.edu

> ...
>     I am trying to format some BLAST databases to use with the BLAST+ tool
> in a local Galaxy installation. According to this:
>     http://wiki.g2.bx.psu.edu/Admin/NGS%20Local%20Setup
>     I have to use the blastdb command with some specific options in order to
> generate the four necessary files (with extensions nhr, nin, nal, nsq). Are
> these commands the same for both nucleotide and protein databases? Are these
> files the same for both kinds of databases?

First of all, the NCBI provides ready to use BLAST databases for NT, NR,
etc on their FTP site:

The makeblastdb command is used to turn a FASTA file into a BLAST
database (this is one of the BLAST+ command line tools). Use the
argument -dbtype nucl or -dbtype prot (default) as appropriate. See
the built in help for more:

makeblastdb -help

For nucleotide databases (which you tell Galaxy about using the
blastdb.loc file) the extensions are nhr, nin, nsd, nsi, nsq plus also
the special nal files for when a database is split into subparts
(usually only done for very large databases like NT).

For protein databases  (which you tell Galaxy about using the
blastdb_p.loc file) the extensions are phr, pin, psd, psi and psq
plus also the special pal files for when a database is split into
subparts (usually only done for very large databases like NR).

Note that to refer to a BLAST database at the command line
(or in Galaxy via blastdb.loc and blastdb_p.loc) you use the
filename WITHOUT any extension.

I hope that helps - you should consult the BLAST+ documentation
for more background information like this.



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