Contig Drawing program?

mathog at mathog at
Fri Jul 26 13:15:58 EST 1996

In article <4t83b6$1g5 at>, pdxark at (Alastair R W Kerr) writes:
>I'm looking for a program (preferably for a dec alpha, but a mac or pc 
>versions would suffice) which would give a graphical represenation of 
>features given their start and stop positions within a contig.  (I've tried
>basic plotting programs, but cannot get sufficiant clarity).
>I'd appreciate any information that anyone could provide.
Well, I'm not quite sure which "features" you are talking about, but if you
are using GCG, then get EGCG and use GELPICTURE.  Here is the blurb: 

     GELPICTURE reads a contig  from  the Fragment  Assembly  database and
     displays a  diagram  of  the  gel alignments  and  a printout of  the
     aligned gel sequences and consensus.  GELPICTURE has been modified to
     include the sequence direction in both sections of the output, and to
     mark  with '=======' any consensus sequence  that is correct  (agrees
     with every fragment) and has been sequenced in both directions.

Or, if you are looking for different information, use GELFIGURE:

     GELFIGURE produces a graphical  summary of  a  contig  in a  fragment
     assembly project.  The output is in four sections: a redundancy plot,
     a diagram of the directoions  and orientations of sequence fragments,
     a restriction map and a plot of open reading frames.

     The  plot is intended both  as a quality guide during the course of a
     sequencing project, and as a final report for a completed assembly.


David Mathog
mathog at
Manager, sequence analysis facility, biology division, Caltech 

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