Making local Database

rvgill · 10-26-2016, 06:33 AM

Hello,

I am making my own database out of fasta files and need help on how to re-format my command line when creating these databases.

makeblastdb -in test.fasta -dbtype nucl -parse_seqids -out testDB

The file type outputs that I receive currently when I run it is :
testDB.nhr
testDB.nin
testDB.nog
testDB.nsd
testDB.nsi
testDB.nsq

What I need is a .nal file to run blast from the error I am receiving. Now do I get a .nal file when I combine multiple databases? I have run blast on a few files and have a couple of folders with all of them organized into it.
How do I combine databases to get one large one with a _____.nal file type?

GenoMax · 10-26-2016, 07:38 AM

Use the blastdb_aliastool. Help available at this page.

maubp · 10-26-2016, 08:05 AM

This is (almost) a duplicate of your other thread, where you have been given some help: http://seqanswers.com/forums/showthread.php?t=72083

GenoMax · 10-26-2016, 08:08 AM

Sounds like here the question is about combining two (or more) separate databases into one alias (if that is what @rvgill meant to ask).

maubp · 10-26-2016, 08:26 AM

In which case its a near duplicate of @rvgill's third thread http://seqanswers.com/forums/showthread.php?t=72192

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10-26-2016, 06:33 AM	#1
rvgill Junior Member Location: Allentown Join Date: Oct 2016 Posts: 6	Making local Database Hello, I am making my own database out of fasta files and need help on how to re-format my command line when creating these databases. makeblastdb -in test.fasta -dbtype nucl -parse_seqids -out testDB The file type outputs that I receive currently when I run it is : testDB.nhr testDB.nin testDB.nog testDB.nsd testDB.nsi testDB.nsq What I need is a .nal file to run blast from the error I am receiving. Now do I get a .nal file when I combine multiple databases? I have run blast on a few files and have a couple of folders with all of them organized into it. How do I combine databases to get one large one with a _____.nal file type?

10-26-2016, 08:05 AM	#3
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	This is (almost) a duplicate of your other thread, where you have been given some help: http://seqanswers.com/forums/showthread.php?t=72083 Last edited by maubp; 10-26-2016 at 08:05 AM. Reason: clarify

10-26-2016, 07:38 AM	#2
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Use the blastdb_aliastool. Help available at this page.

10-26-2016, 08:08 AM	#4
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,080	Sounds like here the question is about combining two (or more) separate databases into one alias (if that is what @rvgill meant to ask).

10-26-2016, 08:26 AM	#5
maubp Peter (Biopython etc) Location: Dundee, Scotland, UK Join Date: Jul 2009 Posts: 1,543	In which case its a near duplicate of @rvgill's third thread http://seqanswers.com/forums/showthread.php?t=72192