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"I have been extremely impressed with SPSOFT's work in optimizing and parallelizing my programs phrap, cross_match and swat. They have outstanding software development expertise, and in my opinion are the premier company working in the area of performance enhancement of sequence analysis software."
Phil Green, University of Washington
SPS SWAT, SPS Cross_Match, and SPS Phrap are based on Phil Green's SWAT, Cross_Match, and Phrap programs. SPSOFT has modified these applications for optimal performance on single and multi-CPU computer systems. See our Support page for information on supported operating systems.
SPS Phrap
See SPS Phrap Benchmarks for more information on scalable gene assembly.
SPS Phrap has been optimized to run faster on a single processor and can scale well as processors are added to a job.
SPS Phrap can dramatically reduce the time it takes to run tough phrap jobs. Our tests demonstrate a 7.2x performance improvement with 8 CPUs. On 2 processor systems, SPS Phrap runs 2.5x faster than UW Phrap v.960731.
SPS SWAT
SPS SWAT is a scalable version of the Smith-Waterman algorithm. SPS SWAT supports linear (affine) gap penalties. It scales linearly as CPUs are added to a job. SPS SWAT scaled 19 times on a 20 processor Sun Ultra Enterprise server.
SPS Cross_Match
Description of Cross_Match (from Phil Green's documentation):
"Cross_Match is a general-purpose utility (based on SWAT, an efficient implementation of the Smith-Waterman algorithm) for comparing any two sets of (long or short) DNA sequences. For example, it can be used to compare a set of reads to a set of vector sequences and produce vector-masked versions of the reads; a set of cDNA sequences to a set of cosmids; contig sequences found by two alternative assembly procedures (e.g. phrap and xbap) to each other; or phrap contigs to the final edited cosmid sequence. It is slower but more sensitive (because it allows gaps) than BLASTN."
SPS Cross_Match runs up to 30% faster than the original Cross_Match when run with a single CPU. SPS Cross_Match runs 3 times faster on a 4 CPU system. SPS Cross_Match has been optimized to work with all-to-all comparisons.
SPSpfam
SPSpfam is a plug-in replacement for Sean Eddy's Hmmpfam module from Hmmer. It provides a significant performance gain over Hmmpfam across the whole spectrum of input query characteristics. For performance comparisons see
SPSsearch
SPSsearch is a refined search replacement for NCBI BLAST. It provides all of the BLAST frame search options with a single or double affine Smith-Waterman alignment algorithm. For the command options see
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