Key Reference Whole Genomes now available for NextGENe® Software
State College PA SoftGenetics announced the availability of whole referencegenomes for use with its NextGENe 2nd generation sequence analysis software. Currently available are Human, Mouse and Rat Genomes in both base space for use with data from the Illumina GA systems, and Roche Genome Sequencer FLX systems and ColorSpace for use with the AB SOLiD Systems. Maize as well as Bovine Genomes are in development and will be available shortly.
Also included with the current version of NextGENe is a whole genome builder which allows users to construct a completely annotated reference of any species for use with NextGENe.
Reference genome annotation includes gene name, chromosome position, reference nucleotide, reported variants, amino acid sequence, dbSNP identification, CDS and mRNA regions as well as a direct link to the dbSNP data base following data processing with NextGENe.
Jonathan Liu, SoftGenetics VP Development states “NextGENe is the first, and we believe only software capable of whole genome alignment of sequence reads from all three next generation platforms providing results in a single view, greatly enhancing the speed and quality of research. NextGENe’s whole genome alignment employs a suffix array to quickly locate the best matching location for each read. As a full suffix array utilizes an inordinate amount of disk space, NextGENe uses the Burrows-Wheeler transform (BWT) to represent the entire suffix array. An efficient rank algorithm allows the software to quickly traverse the suffix array to find the best match for each read. Along with the BWT, the software maintains genome positions at every four base pairs within the genome allowing the software to monitor these locations while traversing the reference genome. This provides a quick and highly accurate alignment. NextGENe aligns both short and long read sequences in as little as 1.5 hours on an 8 core Windows PC.”
For more information or to download a free trial of the software, see [url www.softgenetics.com[/url] or contact the company by e-mail at [email protected]
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SoftGenetics LLC specializes in the development of genetic analysis tools for both research and diagnostic applications; providing
exceptional accuracy in an easy-to-use interface.
Also included with the current version of NextGENe is a whole genome builder which allows users to construct a completely annotated reference of any species for use with NextGENe.
Reference genome annotation includes gene name, chromosome position, reference nucleotide, reported variants, amino acid sequence, dbSNP identification, CDS and mRNA regions as well as a direct link to the dbSNP data base following data processing with NextGENe.
Jonathan Liu, SoftGenetics VP Development states “NextGENe is the first, and we believe only software capable of whole genome alignment of sequence reads from all three next generation platforms providing results in a single view, greatly enhancing the speed and quality of research. NextGENe’s whole genome alignment employs a suffix array to quickly locate the best matching location for each read. As a full suffix array utilizes an inordinate amount of disk space, NextGENe uses the Burrows-Wheeler transform (BWT) to represent the entire suffix array. An efficient rank algorithm allows the software to quickly traverse the suffix array to find the best match for each read. Along with the BWT, the software maintains genome positions at every four base pairs within the genome allowing the software to monitor these locations while traversing the reference genome. This provides a quick and highly accurate alignment. NextGENe aligns both short and long read sequences in as little as 1.5 hours on an 8 core Windows PC.”
For more information or to download a free trial of the software, see [url www.softgenetics.com[/url] or contact the company by e-mail at [email protected]
# # #
SoftGenetics LLC specializes in the development of genetic analysis tools for both research and diagnostic applications; providing
exceptional accuracy in an easy-to-use interface.