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FANGS: high speed sequence mapping for next generation sequencers

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FANGS: high speed sequence mapping for next generation sequencers
Next Generation Sequencing machines are generating millions of short DNA sequences (reads) everyday. There is a need for efficient algorithms to map these sequences to the reference genome to identify SNPs or rare transcripts and to fulfill the dream of personalized medicine. We present a Fast Algorithm for Next Generation Sequencers (FANGS), which dynamically reduces the search space by using q-gram filtering and pigeon hole principle to rapidly map 454-Roche reads onto a reference genome. FANGS is a sequential algorithm designed to find all the matches of a query sequence in the reference genome tolerating a large number of mismatches or insertions/deletions. Using FANGS, we mapped 50000 reads with a total of 25 million nucleotides to the human genome in as little as 23.3 minutes on a typical desktop computer. Through our experiments, we found that FANGS is upto an order of magnitude faster than the state-of-the-art techniques for queries of length 500 allowing 5 mismatches or inser...
Sanchit Misra, Ramanathan Narayanan, Simon Lin, Al
Added 06 Dec 2010
Updated 06 Dec 2010
Type Conference
Year 2010
Where SAC
Authors Sanchit Misra, Ramanathan Narayanan, Simon Lin, Alok N. Choudhary
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