Pairwise Sequence Alignment with Gaps with GPU

Thomas C. Carroll, Jude-Thaddeus Ojiaku, Prudence W.H. Wong
Department of Computer Science, University of Liverpool, UK
4th International Workshop on Heterogenous and Unconventional Cluster Architectures and Applications (HUCAA), 2015

   title={Pairwise Sequence Alignment with Gaps with GPU},

   author={Carroll, Thomas C and Ojiaku, Jude-Thaddeus and Wong, Prudence WH},



Download Download (PDF)   View View   Source Source   



In this paper we consider the pair-wise sequence alignment problem with gaps, which is motivated by the resequencing problem that requires to assemble short reads sequences into a genome sequence by referring to a reference sequence. The problem has been studied before for single gap and bounded number of gaps. For single gap, there was a GPU-based algorithm proposed. In our work we propose a GPU-based algorithm for the bounded number of gaps case. We implemented the algorithm and compare the performance with the CPU-based algorithm in a multithreadded environment; the results are promising with the GPU version achieving a speedup of 30 times.
VN:F [1.9.22_1171]
Rating: 0.0/5 (0 votes cast)

* * *

* * *

TwitterAPIExchange Object
    [oauth_access_token:TwitterAPIExchange:private] => 301967669-yDz6MrfyJFFsH1DVvrw5Xb9phx2d0DSOFuLehBGh
    [oauth_access_token_secret:TwitterAPIExchange:private] => o29ji3VLVmB6jASMqY8G7QZDCrdFmoTvCDNNUlb7s
    [consumer_key:TwitterAPIExchange:private] => TdQb63pho0ak9VevwMWpEgXAE
    [consumer_secret:TwitterAPIExchange:private] => Uq4rWz7nUnH1y6ab6uQ9xMk0KLcDrmckneEMdlq6G5E0jlQCFx
    [postfields:TwitterAPIExchange:private] => 
    [getfield:TwitterAPIExchange:private] => ?cursor=-1&screen_name=hgpu&skip_status=true&include_user_entities=false
    [oauth:protected] => Array
            [oauth_consumer_key] => TdQb63pho0ak9VevwMWpEgXAE
            [oauth_nonce] => 1477508811
            [oauth_signature_method] => HMAC-SHA1
            [oauth_token] => 301967669-yDz6MrfyJFFsH1DVvrw5Xb9phx2d0DSOFuLehBGh
            [oauth_timestamp] => 1477508811
            [oauth_version] => 1.0
            [cursor] => -1
            [screen_name] => hgpu
            [skip_status] => true
            [include_user_entities] => false
            [oauth_signature] => TaF7ueFtSYZHeLK6fw9+5Jl94Z4=

    [url] => https://api.twitter.com/1.1/users/show.json
Follow us on Facebook
Follow us on Twitter

HGPU group

2033 peoples are following HGPU @twitter

HGPU group © 2010-2016 hgpu.org

All rights belong to the respective authors

Contact us: