[Bioperl-l] Retrieving upstream & downstream sequences

Dave Messina David.Messina at sbc.su.se
Mon Jun 14 13:57:30 UTC 2010

Hi Ross,

The code examples here should work:

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


-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.


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