Re: [galaxy-dev] Error with mail in galaxy-dev mailing list

Hi Makis,

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

2012/3/29 Makis Ladoukakis makis4ever@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-request@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: ftp://ftp.ncbi.nlm.nih.gov/blast/db/

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.

Regards,

Peter