Introduction

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 local alignment apply heuristics to reduce the number of possible candidate sequences in the database. However, there is still a need for the alignment of a query sequence to a reduced database. In this paper we present the SW#db tool and a library for fast exact similarity search. Although its running times, as a standalone tool, are comparable to the running times of BLAST, it is primarily intended to be used for exact local alignment phase in which the database of sequences has already been reduced. It uses both GPU and CPU parallelization and was 4-5 times faster than SSEARCH, 6-25 times faster than CUDASW++ and more than 20 times faster than SSW at the time of writing, using multiple queries on Swiss-prot and Uniref90 databases.

Publications

  1. SW#db: GPU-Accelerated Exact Sequence Similarity Database Search.
    Cite this
    Korpar M, Šošić M, Blažeka D, Šikić M, 2015-01-01 - PloS one

Credits

  1. Matija Korpar
    Developer

    University of Zagreb, Faculty of Electrical Engineering and Computing, Croatia

  2. Martin Šošić
    Developer

    University of Zagreb, Faculty of Electrical Engineering and Computing, Croatia

  3. Dino Blažeka
    Developer

    University of Zagreb, Faculty of Electrical Engineering and Computing, Croatia

  4. Mile Šikić
    Investigator

    Bioinformatics Institute, A*STAR, Singapore

Community Ratings

UsabilityEfficiencyReliabilityRated By
0 user
Sign in to rate
Summary
AccessionBT006369
Tool TypeApplication
Category
PlatformsLinux/Unix
Technologies
User InterfaceTerminal Command Line
Download Count0
Country/RegionSingapore
Submitted ByMile Šikić