Related Experiment Videos
CASCAD: a database of annotated candidate single nucleotide polymorphisms associated with expressed sequences
Victor Guryev1, Eugene Berezikov, Edwin Cuppen
1Hubrecht Laboratory, Netherlands Institute for Developmental Biology, Uppsalalaan 8, 3584CT, Utrecht, The Netherlands. guryev@niob.knaw.nl
BMC Genomics
|January 29, 2005
Summary
The CASCAD database provides detailed information on rat and zebrafish single nucleotide polymorphisms (SNPs) discovered through in silico mining. Its advanced search interface facilitates the selection of promising SNPs for experimental research.
Area of Science:
- Genomics
- Bioinformatics
Background:
- Large-scale genome sequencing generates vast amounts of data, necessitating tools for comparative sequence analysis.
- Existing platforms like dbSNP, Ensembl, and UCSC Genome Browser lack extensive annotation and experimental data integration for candidate polymorphisms.
- Identifying and validating useful genetic variations, such as single nucleotide polymorphisms (SNPs), is crucial for experimental research.
Purpose of the Study:
- To present and query candidate SNPs identified through in silico mining of high-throughput sequencing data.
- To provide a centralized resource for detailed information on rat and zebrafish candidate SNPs.
- To facilitate the selection of promising SNPs for experimental validation.
Main Methods:
- Developed the CASCAD database to store and present candidate SNPs from laboratory rat (Rattus norvegicus) and zebrafish (Danio rerio).
- Integrated detailed raw data, extensive annotations, external database links, verification information, and predictions for non-synonymous polymorphisms.
- Implemented a web-based search interface allowing queries based on 27 parameters, custom nucleotide sequences, and cross-linking to other public databases.
Main Results:
- The CASCAD database offers comprehensive data on candidate SNPs, including underlying raw sequencing data.
- Detailed annotation and verification information are provided for each candidate SNP.
- The database supports flexible querying, enabling researchers to find specific SNPs based on various criteria.
Conclusions:
- The CASCAD database provides valuable, detailed information on rat and zebrafish candidate SNPs, including discovery data.
- An advanced web-based search interface offers universal access and supports diverse research utilizing single nucleotide polymorphisms.
- The platform facilitates experimental verification by integrating with primer design and genome assembly tools.