Getting FASTA file of specific interval

[shmibble]

Hi,
Is there anywhere I can search for a sequence of a specific interval (preferably in FASTA format)? For example:
Chromosome 16:14,000,000 - 14,100,000.

Thanks

[GenoMax]

You can retrieve such sequence intervals from BioMart or UCSC genome browser easily. What genome are you working with?

[shmibble]

Thanks! I'm working with the human genome.

[GenoMax]

I also forgot to mention table browser from UCSC above.

If you have a small number of such regions, go to human UCSC genome browser. Type in the interval you want in the gateway page. When the browser displays the region in subsequent page go up to "View" option and choose "DNA". On next page adjust options as needed and then save the DNA sequence that shows up in a file.

[shmibble]

Thanks Geno,

Do you also know if there is a way to do this for many sequences? Perhaps with Biopython?

[dariober]

I think you want bedtools getfasta.

[GenoMax]

twoBitToFa (http://hgdownload.soe.ucsc.edu/admin..._64/twoBitToFa) program from Jim Kent with the 2bit files from UCSC will work as well (e.g. http://hgdownload.soe.ucsc.edu/golde...Zips/hg38.2bit)

[shmibble]

Perfect. Thanks!

[maubp]

Thanks Geno,

Do you also know if there is a way to do this for many sequences? Perhaps with Biopython?

Yes - Biopython will read FASTA files as SeqRecord objects using Bio.SeqIO, and you can slice these records like Python strings to get sub-sequences for given coordinates.

[shmibble]

Good to know. Thanks.