I am blasting cDNA against a protein database and I was wondering whether the default gap parameters, i.e. big penalty for gap existence and small penalty for gap extension, would be the most suitable for this task. For the record, alternative splicing is an abundant feature in my species of study. Should the gap existence penalty be reduced?
In your experience, how important are these parameters in the overall blastx configuration for such a task?
As blastx cuts the alignments into fragments (local alignements) if the score is too low, the exons will be isolated in different local alignements when the introns are long. But, for short introns, it is preferable to lower the gap existence.
Nevertheless, once you have identify interesting proteins with blastx. You should use genewise (see link below) to align those proteins against your cDNA because it will find the introns, even if they are short. It uses dedicated gap penalties.
http://www.ebi.ac.uk/Tools/psa/genewise/
- Badges
- Science topic
- Similar topics
- Biological Science
- Molecular Biology
- Biomolecules
- Nucleic Acids
- DNA