Open Access Highly Accessed Open Badges Methodology article

FAAST: Flow-space Assisted Alignment Search Tool

Fredrik Lysholm1*, Björn Andersson2 and Bengt Persson12

Author Affiliations

1 IFM Bioinformatics and SeRC (Swedish e-Science Research Centre), Linköping University, S-581 83 Linköping, Sweden

2 Department of Cell and Molecular Biology, Science for Life Laboratory, Karolinska Institutet, S-171 77 Stockholm, Sweden

For all author emails, please log on.

BMC Bioinformatics 2011, 12:293  doi:10.1186/1471-2105-12-293

Published: 19 July 2011



High throughput pyrosequencing (454 sequencing) is the major sequencing platform for producing long read high throughput data. While most other sequencing techniques produce reading errors mainly comparable with substitutions, pyrosequencing produce errors mainly comparable with gaps. These errors are less efficiently detected by most conventional alignment programs and may produce inaccurate alignments.


We suggest a novel algorithm for calculating the optimal local alignment which utilises flowpeak information in order to improve alignment accuracy. Flowpeak information can be retained from a 454 sequencing run through interpretation of the binary SFF-file format. This novel algorithm has been implemented in a program named FAAST (Flow-space Assisted Alignment Search Tool).


We present and discuss the results of simulations that show that FAAST, through the use of the novel algorithm, can gain several percentage points of accuracy compared to Smith-Waterman-Gotoh alignments, depending on the 454 data quality. Furthermore, through an efficient multi-thread aware implementation, FAAST is able to perform these high quality alignments at high speed.

The tool is available at webcite