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SpliceMiner: a high-throughput database implementation of the NCBI Evidence Viewer for microarray splice variant
Ari B Kahn1, Michael C Ryan, Hongfang Liu
1Department of Bioinformatics, George Mason University, Fairfax, Virginia, USA. arik@mail.nih.gov <arik@mail.nih.gov>
BMC Bioinformatics
|March 7, 2007
Summary
Alternative splicing generates diverse human transcripts from limited genes. SpliceMiner, a web tool querying the Evidence Viewer Database (EVDB), enables high-throughput analysis of splice variants, improving microarray data interpretation.
Area of Science:
- Bioinformatics
- Genomics
- Molecular Biology
Background:
- The human genome contains fewer genes than expressed transcripts, primarily due to alternative splicing.
- Alternative splicing produces tissue-specific, developmental stage-specific, and condition-specific transcripts.
- Accurate analysis of microarray data and new array design for alternative splicing necessitate probe-level sequence and exon assessment.
Purpose of the Study:
- To develop SpliceMiner, a web interface for querying the Evidence Viewer Database (EVDB).
- To provide a comprehensive, non-redundant compendium of human splice variant data.
- To enable high-throughput batch queries and facilitate probe-to-splice variant mapping.
Main Methods:
- Constructed EVDB as a queryable implementation of the NCBI Evidence Viewer (EV).
- Utilized data from NCBI Entrez Gene and EV, filtering for complete coding sequences and non-redundant splice variants.
- Developed SpliceMiner as a user-friendly web interface for querying EVDB by gene symbol, genomic coordinates, or probe sequence.
Main Results:
- EVDB provides a comprehensive compendium of human splice variant data.
- SpliceMiner supports high-throughput batch queries, unlike the single-query EV.
- SpliceMiner effectively maps probes to specific splice variants.
Conclusions:
- The EVDB/SpliceMiner combination offers a powerful interface for human splice variant information.
- This tool facilitates fluent, high-throughput analysis, enhancing the NCBI Evidence Viewer.
- Integrating EVDB/SpliceMiner into microarray pipelines can improve gene expression data analysis and bioinformatic interpretation, aiding in the identification of splice variant issues.
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