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SFA-SPA is available in binary and source for 64 bit Linux OS.
Craig Venter Institute, San Diego, CA * Corresponding author SPA is available in binary on 64 bit Linux OS. Youngik Yang, Cuncong Zhong, and Shibu Yooseph* J. We also present a new implementation of SPA based on suffix array (SFA-SPA) which runs significantly faster than SPA. Our framework is based on a novel Short Peptide Assembler (SPA) that assembles protein sequences from their constituent peptide fragments identified on short reads. We present a method for reconstructing complete protein sequences directly from NGS metagenomic data. A nucleotide assembly-based strategy does not fare much better since metagenomic assemblies are typically very fragmented and also leave a large fraction of reads unassembled. The metagenomic paradigm offers the opportunity to study protein families, and therefore the metabolic and functional potential, of the constituent microbes in a community.
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