BIP-Align Details
The alignment portion of BIP-Align is a two step process, utilizing both BLAT and SIM4 for mapping the transcripts to the genome.
This approach leverages the speed of BLAT and accuracy of SIM4 to provide the best possible alignment in the shortest amount of time.
The actual steps are:
- Align transcripts to genome using blat
- For each transcript, select the top 10% of all hits.
- For each of these hits, extract the genomic region defined in the BLAT match, plus 50,000 bases upstream and downstream.
- Feed the transcript sequence and hit region into SIM4 for further alignment
- Keep the highest scoring alignment for each transcript, pass to the next step in BIP-Align
Last updated: 12/12/2006
