[Bioperl-l] Retrieving upstream & downstream sequences

[Dave Messina]

Hi Ross,

The code examples here should work:
http://www.bioperl.org/wiki/HOWTO:EUtilities_Cookbook#esummary_-.3E_efetch

except you'll need to change the seq_start and seq_stop parameters to include your extra bases.

i.e.

-seq_start => $start + 1 - 500,
-seq_stop  => $end + 1 + 500,


I haven't tested this — you may need to take the strand information into account when adding or subtracting from the start and end positions.


DAve