@Article{Sinha:Lenser:Jahn:TassD_compr_datab:2010,
  author =	 {Sinha, Rileen and Lenser, Thorsten and Jahn, Niels and 
                  Gausmann, Ulrike and Friedel, Swetlana and Szafranski, Karol 
                  and Huse, Klaus and Rosenstiel, Philip and Hampe, Jochen and 
                  Schuster, Stefan and Hiller, Michael and Backofen, Rolf and 
                  Platzer, Matthias},
  title =	 {{TassDB2} - {A} comprehensive database of subtle 
                  alternative splicing events},
  journal =	 {BMC Bioinformatics},
  year =	 {2010},
  volume =	 {11},
  issn  =        {1471-2105},
  pages =	 {216},
  user =	 {kousik},
  pmid =	 {20429909},
  doi = 	 {10.1186/1471-2105-11-216},
  abstract =	 {BACKGROUND: Subtle alternative splicing events involving 
                  tandem splice sites separated by a short (2-12 nucleotides) 
                  distance are frequent and evolutionarily widespread in 
                  eukaryotes, and a major contributor to the complexity of 
                  transcriptomes and proteomes. However, these events have 
                  been either omitted altogether in databases on alternative 
                  splicing, or only the cases of experimentally confirmed 
                  alternative splicing have been reported. Thus, a database 
                  which covers all confirmed cases of subtle alternative 
                  splicing as well as the numerous putative tandem splice 
                  sites (which might be confirmed once more transcript data 
                  becomes available), and allows to search for tandem splice 
                  sites with specific features and download the results, is a 
                  valuable resource for targeted experimental studies and 
                  large-scale bioinformatics analyses of tandem splice sites. 
                  Towards this goal we recently set up TassDB (Tandem Splice 
                  Site DataBase, version 1), which stores data about 
                  alternative splicing events at tandem splice sites separated 
                  by 3 nt in eight species. DESCRIPTION: We have substantially 
                  revised and extended TassDB. The currently available version 
                  2 contains extensive information about tandem splice sites 
                  separated by 2-12 nt for the human and mouse transcriptomes 
                  including data on the conservation of the tandem motifs in 
                  five vertebrates. TassDB2 offers a user-friendly interface 
                  to search for specific genes or for genes containing tandem 
                  splice sites with specific features as well as the 
                  possibility to download result datasets. For example, users 
                  can search for cases of alternative splicing where the 
                  proportion of EST/mRNA evidence supporting the minor isoform 
                  exceeds a specific threshold, or where the difference in 
                  splice site scores is specified by the user. The predicted 
                  impact of each event on the protein is also reported, along 
                  with information about being a putative target for the 
                  nonsense-mediated decay (NMD) pathway. Links are provided to 
                  the UCSC genome browser and other external resources. 
                  CONCLUSION: TassDB2, available via http://www.tassdb.info, 
                  provides comprehensive resources for researchers interested 
                  in both targeted experimental studies and large-scale 
                  bioinformatics analyses of short distance tandem splice 
                  sites.}
}