@Article{Hiller:Huse:Platzer:Non_based_predi:NAR2005,
  author =	 {Hiller, Michael and Huse, Klaus and Platzer, Matthias and 
                  Backofen, Rolf},
  title =	 {Non-{EST} based prediction of exon skipping and intron 
                  retention events using {Pfam} information},
  journal =	 NAR,
  year =	 {2005},
  volume =	 {33},
  number =	 {17},
  pages =	 {5611-21},
  issn  =        {1362-4962},
  issn  =        {0305-1048},
  user =	 {hiller},
  pmid =	 {16204458},
  publists =     {Michael Hiller and Rolf Backofen and All},
  abstract =	 {Most of the known alternative splice events have been 
                  detected by the comparison of expressed sequence tags (ESTs) 
                  and cDNAs. However, not all splice events are represented in 
                  EST databases since ESTs have several biases. Therefore, 
                  non-EST based approaches are needed to extend our view of a 
                  transcriptome. Here, we describe a novel method for the ab 
                  initio prediction of alternative splice events that is 
                  solely based on the annotation of Pfam domains. Furthermore, 
                  we applied this approach in a genome-wide manner to all 
                  human RefSeq transcripts and predicted a total of 321 exon 
                  skipping and intron retention events. We show that this 
                  method is very reliable as 78% (250 of 321) of our 
                  predictions are confirmed by ESTs or cDNAs. Subsequent 
                  analyses of splice events within Pfam domains revealed a 
                  significant preference of alternative exon junctions to be 
                  located at the protein surface and to avoid secondary 
                  structure elements. Thus, splice events within Pfams are 
                  probable to alter the structure and function of a domain 
                  which makes them highly interesting for detailed biological 
                  investigation. As Pfam domains are annotated in many other 
                  species, our strategy to predict exon skipping and intron 
                  retention events might be important for species with a lower 
                  number of ESTs.}
}