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EASED: Extended Alternatively Spliced EST Database.

Heike Pospisil1, Alexander Herrmann, Ralf H Bortfeldt

  • 1Max-Delbrück-Center for Molecular Medicine, Department of Bioinformatics, Robert-Rössle-Strasse 10, 13125 Berlin, Germany. pospisil@mdc-berlin.de

Nucleic Acids Research
|December 19, 2003
PubMed
Summary
This summary is machine-generated.

A new database, EASED, catalogs alternative splice forms (ASforms) across nine species. It provides detailed profiles including tissue specificity and developmental stage, aiding in the study of gene expression variations.

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Area of Science:

  • Molecular Biology
  • Bioinformatics
  • Genomics

Background:

  • Alternative splicing generates diverse protein isoforms from a single gene.
  • Understanding alternative splicing is crucial for comprehending gene regulation and function.
  • Existing databases may lack comprehensive data on alternative splice forms and their tissue-specific expression.

Purpose of the Study:

  • To establish a comprehensive database of alternative splice forms (ASforms) for nine eukaryotic organisms.
  • To develop methods for defining and analyzing alternative splicing profiles, including tissue specificity.
  • To provide a resource for researchers studying alternative splicing and its implications.

Main Methods:

  • ASforms were identified by comparing expressed sequence tags (ESTs) with mRNA sequences using BLAST.
  • Exon-intron information from Ensembl was integrated to define splice variants.
  • Filtering programs identified deletions/insertions in ESTs indicating alternative splicing.
  • Alternative splicing profiles (NAE, NCE, NSS) and tissue-specific scores were calculated.

Main Results:

  • A database of ASforms was created for nine eukaryotic species.
  • Detailed alternative splicing profiles, including number of alternatively spliced ESTs (NAE) and constitutively spliced ESTs (NCE), were defined for human sequences.
  • Tissue-specific analysis of ASforms was enabled by incorporating EST tissue type information.
  • Splice propensity (NSS) and tissue-specific scores (tissue-NAEs, tissue-NCEs, tissue-NSS) were calculated.

Conclusions:

  • The EASED database provides a valuable resource for studying alternative splicing across eukaryotes.
  • The defined profiles and scores facilitate the analysis of alternative splice form prevalence and tissue specificity.
  • The inclusion of developmental stage and disease information enhances the utility of EASED for diverse research applications.