Does anybody know how to download flanking sequences from a specific coordinate (i.e 3_9835078 where 3 is the chromosome number), in a bulk mode?
I have a list of coordinates corresponding to specific sequence regions in the Arabidopsis genome. I want to get the flanking sequences of this locations (200 bp up and 200 bp down resulting in a 400 bp sequence, for instance).
Thank you in advance!
You can use the substr function in Perl to extract your sequences, since you know the starting position (coordinate-200) and the length (400).
http://perldoc.perl.org/functions/substr.html
Thank you, I was thinking about to avoid the need of downloading the whole genome sequence, but that is a good alternative I can start with.
To whom may be interested, I found a particularly easy way to achive the sequences by using this web:
https://usegalaxy.org/
There you can find this menu: Fetch Alignments/Sequences
And the next option: Extract Genomic DNA using coordinates from assembled/unassembled genomes
Using coordinates gives you the sequence. Easy, fast and useful for ChIP experiments.
You can also retrieve sequence using RSAT ( Regulatory Sequence Analysis Tool ) if you want the non coding sequences
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