FASTA database of human_g1k_v37.fasta

[ashkot]

Hi all,
I want to BLAST using the human_g1k_v37_fasta as database. When i run formatdb on this file and run blast subsequent to that, i get a message stating index file not found.

Can someone please let me know if it's possible to convert this file to FASTA database and if so the command to be used.

Thanks in advance.

Ashwin

[maubp]

In principle there is no reason why human_g1k_v37_fasta cant be used as a BLAST database.

I suggest reading this: Ten Simple Rules for Getting Help from Online Scientific Communities

http://www.ploscompbiol.org/article/info%3Adoi%2F10.1371%2Fjournal.pcbi.1002202

For a start, which version of BLAST are you using, which OS are you using, and what were the commands you ran to build the database, and to execute the BLAST search, and what was the EXACT error message?

[ashkot]

Follow up info

Thanks for link to that article.

I am using blast-2.2.25+ on Ubuntu and formatdb -n human_g1k_v37_fasta.fasta

The exact error i get when i try to run blastn is index file not found for database human_g1k_v37_fasta

Thanks.

Ashwin

[maubp]

What files did formatdb create? And why are you using formatdb - that's from legacy BLAST, you should be using makeblastdb for BLAST+

[ashkot]

Files and still getting error

Right, so i used makeblastdb as follows

makeblastdb -in human_g1k_v37.fasta -title human_g1k_v37

it made three files each with
.psq, .phr and .pin file extensions

i am trying to execute blastn as follows

blasntn -query {query file} -db human_g1k_v37 -out Results.txt -strand plus

I am getting error 'No index or alias found for database human_g1k_v37'

thanks

[maubp]

Right, so i used makeblastdb as follows

makeblastdb -in human_g1k_v37.fasta -title human_g1k_v37

it made three files each with
.psq, .phr and .pin file extensions

From the extensions that made a protein database (which is the default behaviour IIRC). There is an option to makeblastdb to make a nucleotide database which you'll need to use.

[ashkot]

Update

Thanks, a lot, BLAST is working now. It had to do with the database being not available in the right format.