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ASPicDB: a database resource for alternative splicing analysis.

T Castrignanò1, M D'Antonio, A Anselmo

  • 1Consorzio Interuniversitario per le Applicazioni di Supercalcolo per Università e Ricerca, CASPUR, Rome, Italy.

Bioinformatics (Oxford, England)
|April 5, 2008
PubMed
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ASPicDB offers reliable alternative splicing annotations for human genes, improving transcriptome complexity analysis. This database provides enhanced data access and functional insights into splicing patterns in normal and cancer cells.

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Alternative splicing significantly expands transcriptome and proteome complexity in humans.
  • Existing resources for alternative splicing analysis have limitations in computational methods, annotation scope, and data accessibility.
  • There is a need for comprehensive and user-friendly tools for alternative splicing research.

Purpose of the Study:

  • To develop ASPicDB, a database providing reliable alternative splicing annotations for human genes.
  • To offer functional annotations for predicted splicing isoforms.
  • To enhance data query and download facilities for researchers.

Main Methods:

  • Genome-wide application of the ASPic algorithm for splice-site detection and full-length transcript modeling.

Related Experiment Videos

  • Utilizing multiple alignments of gene-related transcripts to genomic sequences for improved prediction accuracy.
  • Integrating EST sequences and library source annotations for tissue-specific splicing analysis.

    • Main Results:

    • ASPicDB provides reliable annotations of alternative splicing patterns and functional insights into splicing isoforms.
    • The database features enhanced query and download capabilities for genes, transcripts, and introns.
    • Results are presented in tabular and graphical formats for comprehensive assessment of alternative splicing implications.
    • Includes tissue-specific splicing patterns from normal and cancer cells.

    Conclusions:

    • ASPicDB serves as a valuable resource for exploring human alternative splicing.
    • The database facilitates detailed analysis of splicing patterns and their functional consequences.
    • Regular updates and enhanced features make ASPicDB a dynamic tool for the research community.