makeblastdb

[Meligethes]

Hi !

Simple question, but i just can't find the answer :

What is the difference between "-out" and "-title" in makeblastdb

Thanks

[Meligethes]

It seems that "-title" is the way to give the database another name that inputfile.nhr/nsq/nih ??

[maubp]

The -title is free text for a description (shown in the plain text or HTML output for example).

The -out is the base of the filename for the database, which is how you would refer to this database at the command line when you search against it.

Both default to being based on the input filename.

[Meligethes]

Thanks, it makes it more clear now

Another thing, how can I put a kind of alias in order to have shorter commands like :

blastn -query file.fa -db /path/to/dbname

=> blastn -query file.fa -db dbname

The blastn man tells about some .ncbirc in home directory. But I don't understand how to correctly put things in it.

[maubp]

I assume you are using Linux? So you've read http://www.ncbi.nlm.nih.gov/books/NB....Configuration and didn't understand it?

Have you created a ".ncbirc" file in your home directory (this starts with a dot so will be hidden by default) containing this:

[BLAST]
BLASTDB=/path/to

where that path is where you are putting your databases?

[Meligethes]

Yes I created the file.

The path to my DB is :
/media/meligethes-2/db/VSSC/
I have several databases created

But alias does not work.

Here is my .ncbirc file :

[BLAST]
BLASTDB=/media/meligethes-2/db/BS13
BLASTDB=/media/meligethes-2/db/VSSC
BLASTDB=/media/meligethes-2/db/PBEE
BLASTDB=/media/meligethes-2/db/TCAS

[Meligethes]

OK, i think blast does not take my .ncbirc file in consideration because he first finds another place where databases are defined :

# blastn -query 1F.fa -db VSSC -num_threads 4 -out test
BLAST Database error: No alias or index file found for nucleotide database [VSSC] in search path [/media/meligethes-2/lab/1F::/media/meligethes-2/db/TCAS:]

[maubp]

I'm guessing you mean you have a folder /media/meligethes-2/db/ which contains four databases (BS13, VSSC, PBEE, TCAS), in which case try:

[BLAST]
BLASTDB=/media/meligethes-2/db/

You can also control this via the BLASTDB environment variable.