[Bioperl-l] Starting from scratch, a trivial problem?

JAMES IBEN jiben at jhu.edu
Fri May 7 14:16:58 EDT 2004

  Hello.  I'm relatively new to programming in perl to begin with, so I apologize for the foolish question.
  I would like to write a program to pull genomic sequences and clip out a specific intergenic region in species where it exists, but I am running into difficulty trying to incorporate the bioperl modules into my script to accomplish this. This coupled with a  grasp of only the the ability to script the most rudimentary programs has left me at a bit of a loss.
  I believe the program should run with this rough outline unless someone has a more informed opinion:

-Obtain sequence from online databank
-Search annotations for sequential occurrence of gene X and gene Y (or gene Y and gene X)
-Print to output file Sequence ID and sequence occurring between addresses of X and Y
-loop to next sequence

  I would be very grateful if someone could please point me in the direction of perhaps a similar example script or a lower-level resource.  It seems like it would be a fairly trivial problem.

Thanks for your time,

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