Abstract

The search for homologous RNA molecules---sequences of RNA that might behave simiarly due to similarity in their physical (secondary) structure---is currently a computationally intensive task. Moreover, RNA sequences are populating genome databases at a pace unmatched by gains in standard processor performance. While software tools such as Infernal can efficiently find homologies among RNA families and genome databases of modest size, the continuous advent of new RNA families and the explosive growth in volume of RNA sequences necessitate a faster approach.
This work introduces two different architectures for accelerating the task of finding homologous RNA molecules in a genome database. The first architecture takes advantage of the tree-like configuration of the covariance models used to represent the consensus secondary structure of an RNA family and converts it directly into a highly …

Date

September 1, 2010

Authors

James Moscola, Ron K Cytron, Young H Cho

Journal

ACM Transactions on Reconfigurable Technology and Systems (TRETS)

Volume

3

Issue

3

Pages

1-44

Publisher

ACM