BIP-Splice General Use Cases
Purpose: To provide an alternative splicing analysis database for a single organism. This database aims to be as complete as possible, capturing the entire transcriptome and enabling a researcher to query based on any arbitrary criteria.
Requirements:
- DBMS installed and ready to use. Supported systems are PostgreSQL and MySQL, DB2 to be added
- SGE system installed and configured
- BIP-Align and BIP-Splice tools
Usage:
- Download genome data from desired source. UCSC is one example of a suitable data source. Genome data must be in separte fasta files.
- Download transcript (cDNA, mRNA and EST data) from desired data sources. Example sources are GenBank, dbEST and UniGene
Download instructions - Use BIP-Align to create the initial database. This database will hold all input transcripts and their alignments.
- Use BIP-Splice to update the initial database with transcript clustering and splice analysis data.
- Query database according to researcher's needs.
For any comments or suggestions, send an e-mail at: BIP_FEEDBACK@asu.edu
