SW#db: GPU-Accelerated Exact Sequence Similarity Database Search.

ABSTRACT: In recent years we have witnessed a growth in sequencing yield, the number of samples sequenced, and as a result-the growth of publicly maintained sequence databases. The increase of data present all around has put high requirements on protein similarity search algorithms with two ever-opposite goals: how to keep the running times acceptable while maintaining a high-enough level of sensitivity. The most time consuming step of similarity search are the local alignments between query and database sequences. This step is usually performed using exact local alignment algorithms such as Smith-Waterman. Due to its quadratic time complexity, alignments of a query to the whole database are usually too slow. Therefore, the majority of the protein similarity search methods prior to doing the exact l

SUBMITTER: Korpar M 

PROVIDER: S-EPMC4699916 | biostudies-literature | 2015

REPOSITORIES: biostudies-literature