Subject: | Alternative Splicing |
Presenter: | Baharak Rastegari |
Paper: | " A Non-EST-Based Method for Exon-Skipping Prediction " |
  | by Sorek R, Shemesh R, Cohen Y, Basechess O, Ast G, and Shamir R. |
Abstract |
A Non-EST-Based Method for Exon-Skipping Prediction
It is estimated that between 35% and 74% of all human genes can undergo
alternative splicing. Currently, the most efficient methods for large-scale
detection of alternative splicing use expressed sequence tags (ESTs) or
microarray analysis. As these methods merely sample the transcriptome,
splice variants that do not appear in deeply sampled tissues have a low
probability of being detected. We present a new method by which we can
predict that an internal exon is skipped (namely whether it is a
cassette-exon) merely based on its naked genomic sequence and on the
sequence of its mouse ortholog. No other data, such as ESTs, are required
for the prediction. Using our method, which was experimentally validated,
we detected hundreds of novel splice variants that were not detectable
using ESTs. We show that a substantial fraction of the splice variants
in the human genome could not be identified through current human EST or
cDNA data.
Reference:
Sorek R, Shemesh R, Cohen Y, Basechess O, Ast G, and Shamir R. (2004).
A non-EST-based method for exon-skipping prediction. Genome Res.
Aug; 14(8):1617-1623.
The paper is available at http://egweb.bcgsc.bc.ca/journal_club/2004_2005/pdf/short_report_041008.pdf
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