Graphical Processing Unit - Supported RNA Secondary Structure Comparison

This study is part of our perpetual effort to develop improved RNA secondary structure analysis tools and databases. In this work we present a new Graphical Processing Unit (GPU)-based RNA structural analysis framework that supports fast multiple RNA secondary structure comparison for very large databases. A search-based secondary structure comparison algorithm deployed in RNASSAC website helps bioinformaticians find common RNA substructures from the underlying database. The algorithm performs two levels of binary searches on the database. Its time requirement is affected by the database size. Experiments on the RNASSAC website show that the algorithm takes seconds for a database of 4,666 RNAs. For example, it takes about 4.4 sec for comparing 25 RNAs from this database. In another case, when many non-overlapping common substructures are desired, a heuristic approach requires as long as 85 sec in comparing 40 RNAs from the same database. The comparisons by this sequential algorithm takes at least 50% more time when RNAs are compared from the database of several millions of RNAs. The most recently curated databases already have millions of RNA secondary structures. The improvement in run-time performance of comparison algorithms is necessary. This study present a GPU-based RNA substructure comparison algorithm with which running time for multiple RNA secondary structures remains feasible for large databases. Our new parallel algorithm is 12 times faster than the CPU version (sequential) comparison algorithm of the RNASSAC website. The response time significantly reduces towards development of a realtime RNA comparison web service for bioinformatics community.