intron splice-junctions software

Jill Kellogg jkellogg at
Mon Aug 18 18:53:03 EST 1997

Dear Els,

MacVector will do this of course and much more.  One thing about plant introns
is that a splice site is not enough to determine if a splice will occur or not. 
AT rich regions are preferentially spliced our, so introns can be generally
located buy analyzing the base composition of the sequence.  (See the paper, "3'
Splice Site Selection in Dicot Plant Nuclei Is Position Dependent", by Lou,
McCullough and Schuler, in Molecular and Cellular Biology, Aug 1993, p. 4485-
4493.) MacVector will also perform base composition analysis.  Sorry, but I am
not familiar with non-Mac software if that is what you are looking for.  There
is a great little journal called Biotechnology Software and Internet Journal
which does regular reviews of Mol Bio/Biotech software for both Non-Mac's and
Mac's.  See if anyone you know gets it, and has back copies.

Good luck finding you introns,

Jill Kellogg
Research Associate
Agritope, Inc
Portland, OR

Subject: intron splice-junctions software
From:    Van Geldre Els <Els.VanGeldre at> at INTERNET
Date:    8/6/97  3:18 AM

Dear all,
  First of all I would like to thank you for all previous answers and
  suggestions to my questions. Secondly, I would like to ask you the
  following. Does someone know wether there exists (and where I can find
  it) a program that is capable to find splice junctions in a given gDNA
  sequence ? I have some PCR products derived from gDNA of plants (about
  1kb). I would like to derive the protein sequence from these DNA
  sequences, but only the exons without the introns. I found such a
  program specific for Arabidopsis, but I wonder wether there exists 
  more general for other plants.
  Thank you for answering,

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