High-speed Multiple Sequence Alignment on a reconfigurable platform

Abstract

Progressive alignment is a widely used approach to compute multiple sequence alignments (MSAs). However, aligning several hundred sequences by popular progressive alignment tools requires hours on sequential computers. Due to the rapid growth of sequence databases biologists have to compute MSAs in a far shorter time. In this paper we present a new approach to MSA on reconfigurable hardware platforms to gain high performance at low cost. We have constructed a linear systolic array to perform pairwise sequence distance computations using dynamic programming. This results in an implementation with significant runtime savings on a standard FPGA.

Addresses

School of Computer Engineering, Nanyang Technological University, Singapore. tim.oliver@gmail.com

Autoren

Tim Oliver
Bertil Schmidt
Douglas Maskell
Darran Nathan
Ralf Clemens

DOI

10.1504/ijbra.2006.011038

eISSN

1744-5493

Externe Identifier

PubMed Identifier: 18048180

Open access

false

ISSN

1744-5485

Ausgabe der Veröffentlichung

4

Zeitschrift

International journal of bioinformatics research and applications

Schlüsselwörter

Cluster Analysis
Sequence Alignment
Sequence Analysis, Protein
Computational Biology
Algorithms
Computing Methodologies
Signal Processing, Computer-Assisted
Software
User-Computer Interface
Databases, Protein

Sprache

eng

Medium

Print

Paginierung

394 - 406

Datum der Veröffentlichung

2006

Status

Published

Datum der Datenerfassung

2007

Titel

High-speed multiple sequence alignment on a reconfigurable platform.

Sub types

Journal Article

Ausgabe der Zeitschrift

2

Datenquelle: Europe PubMed Central

Abstract

Progressive alignment is a widely used approach to compute multiple sequence alignments (MSAs). However, aligning several hundred sequences by popular progressive alignment tools requires hours on sequential computers. Due to the rapid growth of sequence databases biologists have to compute MSAs in a far shorter time. In this paper we present a new approach to MSA on reconfigurable hardware platforms to gain high performance at low cost. We have constructed a linear systolic array to perform pairwise sequence distance computations using dynamic programming. This results in an implementation with significant runtime savings on a standard FPGA.

Autoren

Tim Oliver
Bertil Schmidt
Douglas Maskell
Darran Nathan
Ralf Clemens

Autoren-URL

https://www.ncbi.nlm.nih.gov/pubmed/18048180

DOI

10.1504/IJBRA.2006.011038

ISSN

1744-5485

Ausgabe der Veröffentlichung

4

Zeitschrift

Int J Bioinform Res Appl

Schlüsselwörter

Algorithms
Cluster Analysis
Computational Biology
Computing Methodologies
Databases, Protein
Sequence Alignment
Sequence Analysis, Protein
Signal Processing, Computer-Assisted
Software
User-Computer Interface

Sprache

eng

Country

Switzerland

Paginierung

394 - 406

PII

AR4LXR9XUKBDK8XH

Datum der Veröffentlichung

2006

Status

Published

Datum, an dem der Datensatz öffentlich gemacht wurde

2008

Titel

High-speed multiple sequence alignment on a reconfigurable platform.

Sub types

Journal Article

Ausgabe der Zeitschrift

2

Datenquelle: PubMed

Autoren

Timothy F Oliver
Bertil Schmidt
Douglas L Maskell
Darran Nathan
Ralf Clemens

Zeitschrift

Int. J. Bioinform. Res. Appl.

Artikelnummer

4

Paginierung

394 - 406

Datum der Veröffentlichung

2006

Titel

High-speed Multiple Sequence Alignment on a reconfigurable platform.

Ausgabe der Zeitschrift

2

Datenquelle: DBLP

High-speed Multiple Sequence Alignment on a reconfigurable platform

Werkzeuge