Contig Drawing program?

mathog at seqaxp.bio.caltech.edu mathog at seqaxp.bio.caltech.edu
Fri Jul 26 13:15:58 EST 1996


In article <4t83b6$1g5 at paperboy.ccc.nottingham.ac.uk>, pdxark at evol.nott.ac.uk (Alastair R W Kerr) writes:
>Hi, 
>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.

Regards,

David Mathog
mathog at seqaxp.bio.caltech.edu
Manager, sequence analysis facility, biology division, Caltech 




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