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Help to use formatdb - (Dec/30/2008 )

I am just a new to Bioinformatics. Now, I am currently conducting a project which require me to use the formatdb to format the nr database. I have downloaded formatdb from blast standalone software. however, i don't know how to operate the formatdb! Can anybody help me? Help i need the detail of steps involve in using formatdb to format nr database.

-Aaron22-

formatdb is a command-line program used to create BLAST databases from a FASTA or ASN.1 file of either nucleotide or amino acid sequences. The directions on how to use it are included in the readme file distributed with the program (a copy is here).

Is this what you're trying to do? Create a custom BLAST database from a collection of sequences? The "nr" database you mention is huge -- and it's available online. If you need a local copy of it in BLAST form, you can download that directly (see here) and skip the formatdb step.

-HomeBrew-

QUOTE (HomeBrew @ Dec 31 2008, 09:51 AM)
formatdb is a command-line program used to create BLAST databases from a FASTA or ASN.1 file of either nucleotide or amino acid sequences. The directions on how to use it are included in the readme file distributed with the program (a copy is here).

Is this what you're trying to do? Create a custom BLAST database from a collection of sequences? The "nr" database you mention is huge -- and it's available online. If you need a local copy of it in BLAST form, you can download that directly (see here) and skip the formatdb step.



Thanks a lot for ur reply! I think I should download the nr database directly from the website! Wat i downloaded last time is a non-blast form! I will try it!

BUT, which database should I download? nr.00.tar.gz , nr.01.tar.gz , or nr.02.tar.gz?


-Aaron22-

It's in the README file (emphasis added):

QUOTE
Large databases are formatted in multiple 1 Gigabytes volumes, which are named using the database.##.tar.gz convention. All relevant volumes are required. An alias file is provided so that the database can be called using the alias name without the extension (.nal or .pal). For example, to call est database, simply use "-d est" option in the commandline (without the quotes).


Is there a reason you want a local copy of this database, rather than using the BLAST interface available on the web?

-HomeBrew-

QUOTE (HomeBrew @ Dec 31 2008, 01:49 PM)
It's in the README file (emphasis added):

QUOTE
Large databases are formatted in multiple 1 Gigabytes volumes, which are named using the database.##.tar.gz convention. All relevant volumes are required. An alias file is provided so that the database can be called using the alias name without the extension (.nal or .pal). For example, to call est database, simply use "-d est" option in the commandline (without the quotes).


Is there a reason you want a local copy of this database, rather than using the BLAST interface available on the web?


Actually, I am using a software called MolIDE to construct 3D model of protein. I want to do the allignment by the software by using psi-blast inside the software! The psi-blast was modified that it can search the nr database first and then use the result to search pdbaa database!

-Aaron22-