Produce fasta file from genome coordinates

Question

[claudio]

I wish to query blastn using genome coordinates rather than a specific gene but it seems that I would need a fasta sequence in order to do so. Is there a way to generate a fasta sequence from genomic coordinates such as the following: chr11:5,300,000-5,600,000

[cpad0112]

if you have reference genome as fasta file, use samtools faidx

[lieven.sterck]

you can use the built-in functionality of blast to do this.

check out the blastdbcmd command (entry + range )

[claudio]

Is there a way to do this from the ncbi website or another website because I don't have the capacity on my pc to download large database files.

[lieven.sterck]

OK, valid remark indeed.

You can download a fasta version of your hits from the NCBI blast output webpage. Not sure if you can just 'randomly' get a range .