Produce fasta file from genome coordinates
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
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claudio •
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if you have reference genome as fasta file, use
samtools faidxyou can use the built-in functionality of blast to do this.
check out the
blastdbcmdcommand (entry + range )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.
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 .