New program:
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RNASPL - Prediction of exon-exon junction positions in
cDNA sequences
Department of Cell Biology, Baylor College of Medicine
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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.
