EASED: Extended Alternatively Spliced EST Database

We established a database of alternative splice forms (ASforms) for nine eukaryotic organisms. ASforms are defined by comparing high-scoring ESTs with mRNA sequences using BLAST, taking known exon-intron information (from the Ensembl database). Filtering programs compare the ends of each aligned sequence pair for deletions or insertions in the EST sequence, which indicate the existence of alternative splice forms with respect to the exon-intron boundaries. Moreover, we defined the alternative splice profile of each human sequence. It indicates the number of alternatively spliced ESTs (NAE), the number of constitutively spliced ESTs (NCE) as well as the number of alternative splice sites (NSS) per mRNA. NAE and NCE correspond to the EST coverage and can be used as a quality indicator for the predicted alternative splice variants. The NSS value specifies the splice propensity of a gene. Additionally, the tissue type information of all ESTs was included. This allows (i) restriction of the search to certain tissues and (ii) calculation of the tissue-NAEs, tissue-NCEs and tissue-NSS. These scores are suitable for the estimation of tissue specificity of certain ASforms. Furthermore, the developmental stage and disease information of the ESTs is available. EASED is accessible at http://eased.bioinf.mdc-berlin.de/.

[1]  D. Haussler,et al.  A physical map of the human genome , 2001, Nature.

[2]  Martin Vingron,et al.  SpliceNest: visualizing gene structure and alternative splicing based on EST clusters , 2002 .

[3]  M. Gelfand,et al.  Frequent alternative splicing of human genes. , 1999, Genome research.

[4]  Juha Muilu,et al.  Conservation of human alternative splice events in mouse. , 2003, Nucleic acids research.

[5]  Christopher J. Lee,et al.  A genomic view of alternative splicing , 2002, Nature Genetics.

[6]  Y.-H. Huang,et al.  PALS db: Putative Alternative Splicing database , 2002, Nucleic Acids Res..

[7]  Christopher J. Lee,et al.  Genome-wide detection of alternative splicing in expressed sequences of human genes , 2001, Nucleic Acids Res..

[8]  W. Gish,et al.  Gene structure prediction and alternative splicing analysis using genomically aligned ESTs. , 2001, Genome research.

[9]  Yi Xing,et al.  ASAP: the Alternative Splicing Annotation Project , 2003, Nucleic Acids Res..

[10]  Kevin Burrage,et al.  ISIS, the intron information system, reveals the high frequency of alternative splicing in the human genome , 2000, Nature Genetics.

[11]  W. James Kent,et al.  The Intronerator: exploring introns and alternative splicing in Caenorhabditis elegans , 2000, Nucleic Acids Res..

[12]  P. Bork,et al.  Alternative splicing and genome complexity , 2002, Nature Genetics.

[13]  Thangavel Alphonse Thanaraj A clean data set of EST-confirmed splice sites from Homo sapiens and standards for clean-up procedures , 1999, Nucleic Acids Res..

[14]  Alistair G. Rust,et al.  Ensembl 2002: accommodating comparative genomics , 2003, Nucleic Acids Res..

[15]  Ian Korf,et al.  MaskerAid : a performance enhancement to RepeatMasker , 2000, Bioinform..

[16]  The International HapMap Consortium,et al.  A physical map of the human genome , 2001 .