Poster Session
Hardware accelerated iterative sequence profile search
By Roland Luethy
Ph.D., TimeLogic Corp.
Iterative sequence database searches have been shown to increase sensitivity
for detection of distant similarity between protein sequences. The most
popular tool for iterative searches is currently PSI-BLAST. Methods using
dynamic programming alignment techniques have been generally considered to
be too time consuming for iterative searches. TimeLogicıs DeCypher system
accelerates such dynamic programming algorithms and makes it feasible to
test iterative profile searches. We have implemented an iterative search
method using position specific scoring matrices (PSSM) that were created in
a similar fashion to the ones used in PSI-BLAST. These PSSMs were used with
TimeLogicıs profilesearch implementation on the DeCypher accelerated
bioinformatics system. To test the method, the sequences of the ASTRAL SCOP
database with less than 40% identity were used to make PSSMs and the
resulting profiles were then used to search the same database. Receiver
operating characteristics curves were generated to compare the results using
the dynamic algorithm based method and PSI-BLAST. Matches were considered
correct positives if the superfamily assignment of the query and the match
from SCOP were identical. The new method demonstrates an increased sensitivity at low error rates and -- with fixed error rate of 1% -- it finds 11% more true positives than PSI-BLAST.
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