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Bioinformatics Advance Access originally published online on August 12, 2009
Bioinformatics 2009 25(19):2514-2521; doi:10.1093/bioinformatics/btp486
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© 2009 The Author(s)
This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

PerM: efficient mapping of short sequencing reads with periodic full sensitive spaced seeds

Yangho Chen , Tade Souaiaia and Ting Chen *

Program in Computational Biology and Bioinformatics, University of Southern California, 1050 Childs Way, Los Angeles, CA 90089-2910, USA

*To whom correspondence should be addressed.


  Abstract

Motivation: The explosion of next-generation sequencing data has spawned the design of new algorithms and software tools to provide efficient mapping for different read lengths and sequencing technologies. In particular, ABI's sequencer (SOLiD system) poses a big computational challenge with its capacity to produce very large amounts of data, and its unique strategy of encoding sequence data into color signals.

Results: We present the mapping software, named PerM (Periodic Seed Mapping) that uses periodic spaced seeds to significantly improve mapping efficiency for large reference genomes when compared with state-of-the-art programs. The data structure in PerM requires only 4.5 bytes per base to index the human genome, allowing entire genomes to be loaded to memory, while multiple processors simultaneously map reads to the reference. Weight maximized periodic seeds offer full sensitivity for up to three mismatches and high sensitivity for four and five mismatches while minimizing the number random hits per query, significantly speeding up the running time. Such sensitivity makes PerM a valuable mapping tool for SOLiD and Solexa reads.

Availability: http://code.google.com/p/perm/

Contact: tingchen{at}usc.edu

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Joaquin Dopazo

Received on May 14, 2009; revised on July 18, 2009; accepted on August 7, 2009

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