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Old 01-29-2015, 12:47 AM   #1
GSviral
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Default Creating a Command Line BLAST+ Database

Hey guys,

I am relatively new to linux and command line and have a basic understanding of the basic commands in regards to the terminal.

What I want to do is set up local BLAST+ databases so I can BLAST hundreds of sequences against the blastx or blastn databases.

So far I have downloaded the latest databases, extracted them via gunzip, and copied them into my usr/local/bin folder. I believe this allows me to run BLAST applications from anywhere.

I do not know where to go next. Do I have to format the blastx and blastn databases before I can blast my sequences? If so can any of you please point me in the right direction in how to do this?

Any help is appreciated, thank you very much!

Ryan.
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Old 01-29-2015, 04:23 AM   #2
GenoMax
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As long as you downloaded the pre-formatted databases from (ftp://ftp.ncbi.nlm.nih.gov/blast/db/) you can use them directly with blast+. You have also got the executables for your OS: ftp://ftp.ncbi.nlm.nih.gov/blast/exe...last+/LATEST/?

Follow the command line manual for blast to start your analysis: http://www.ncbi.nlm.nih.gov/books/NBK1763/

Keep realistic expectations if you are going to do the blast locally, specially if you have modest hardware (post specs if you need any specific comments on that). It will take time to blastx several hundred sequences against nr.
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Old 01-29-2015, 04:41 AM   #3
GSviral
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Hello GenoMax,

Thanks for the help. To begin I have downloaded the pre-formatted nt database.

Once I unzip all the files associated with the nt database do I place them in the same directory as I have placed the BLAST+ executables? Once this is done I assume I will be able to run a search using one of my fasta files against the nt database.

Thank you,

Ryan.
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Old 01-29-2015, 05:22 AM   #4
GenoMax
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Quote:
Originally Posted by GSviral View Post
Hello GenoMax,

Thanks for the help. To begin I have downloaded the pre-formatted nt database.

Once I unzip all the files associated with the nt database do I place them in the same directory as I have placed the BLAST+ executables? Once this is done I assume I will be able to run a search using one of my fasta files against the nt database.

Thank you,

Ryan.
You can put the database files where ever convenient. When you start your blast you will specify DB location by using the -db command line option and providing the path to the files. All the pieces for a set (numerically named files) need to be in the same directory and you only need to use the base name i.e. nr (do not include the numbers)
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