RT Journal
A1 Sorek, Rotem
A1 Shemesh, Ronen
A1 Cohen, Yuval
A1 Basechess, Ortal
A1 Ast, Gil
A1 Shamir, Ron
T1 A Non-EST-Based Method for Exon-Skipping Prediction
JF Genome Research 
JO Genome Research 
YR 2004 
FD August 01 
VO 14 
IS 8 
SP 1617 
OP 1623 
DO 10.1101/gr.2572604 
UL http://genome.cshlp.org/content/14/8/1617.abstract 
AB 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.