RNASPL - Program for redicting exon-exon junction positions in cDNA sequences
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.
We can not predict exon-exon junction position with very high accuracy, because some important information is being lost during splicing. We predict positions marked by '*', where 75% of potential exon-exon junctions are localized. Additionally, we mark '-' positions where exon-exon junctions atr absent with probability about 90%. We recommend to select primer sequences in continuous '-' regions that do not cross '*' or ' ' positions.
Solovyev V.V.,Salamov A.A., Lawrence C.B.
RNASPL output: First line - name of your sequence Second line - your sequence 3d line - '*' shows potential exon-exon junction position (Pr > 0.75)
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