Exon-exon junctions in cDNA by BCM Gene-finder

Victor V. Solovyev solovyev at cmb.bcm.tmc.edu
Fri Feb 10 14:46:18 EST 1995


New program:
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	RNASPL - Prediction of exon-exon junction positions in
		 cDNA sequences
 	Department of Cell Biology, Baylor College of Medicine
=========================================================================
	Analysis of human cDNA sequences is available through 

 WWW BCM Human Genome Center and Search launcher Home page
URL:http://kiwi.imgen.bcm.tmc.edu:8088/search-launcher/launcher.html

for accsess to Gene-finder prediction Help files and programs.
->  BCM Gene Finder

Description:
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   Recognition of exon-exon junctions in cDNA may be very useful for 
gene sequencing when starting with a sequence of cDNA clone. In a given 
cDNA sequence we need to select sites for PCR primers that (hopefully) 
lie in adjacent exons. 
   Prediction is performed by linear discriminant function combining 
characteristics describing  tipical sequences around exon-exon junctions.

  The method is described in 
  Solovyev V.V.,Salamov A.A., Lawrence C.B.
   Predicting internal exons by oligonucleotide composition and 
   discriminant analysis of spliceable open reading frames. 
  (Nucl.Acids Res.,1994, 22,24, 5156-5163).

Accuracy:
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We can not predict exon-exon junction position with very high accuracy,
because some information was lost after splicing. We predict positions
marked by '*', where 75% of potential exon-exon junctions are localized. 
Additionally, we mark '-' positions where exon-exon junctions absent with
probability about 90%.
   We recommend to select primer sequences in continuous '-' regions,
that do not cross '*' or ' ' positions.





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