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Old 06-22-2009, 08:01 AM   #1
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Location: pa

Join Date: Apr 2009
Posts: 32
Default Whole Large Genome Alignment with Annotation

Hi here is information on a new function in NextGENe software, if you would like a trial of the software or more information please contact me:

Whole Genome Alignment of 2nd Generation Sequencing Reads added to NextGENe® Software

State College PA SoftGenetics announced the addition of a rapid whole genome alignment (WGA) function to its NextGENe software packages which is compatible with data from the Roche Genome Sequencer, Life Technologies SOLiD™ System and Illumina® Genome Analyzer. Based upon the accepted Burrows-Wheeler transform algorithm, NextGENe adds several key additional technologies to provide fast, accurate alignment of short sequence reads to a whole large genome such as the human, mouse and rat genomes.

NextGENe’s WGA method is the first capable of aligning Roche Genome Analyzer reads which often contain homopolymer errors to a large genome at high speed with greater than 90% accuracy. Shorter reads from the Illumina and SOLiD system are aligned in approximately 2 hours on a quad core desk top system.

NextGENe’s Genome Viewer provides annotated results in an easily navigable single view which indicates genome position, found variants, db SNP number, amino acid sequence, cDNA, exon information among others allowing review and confirmation. NextGENe then provides a multiplicity of reporting and exporting options.

Jonathan Liu, SoftGenetics VP of development stated “The Whole Genome Alignment capability of NextGENe is the result of numerous customer driven requests and collaborations. Combined with our unique error reduction Condensation Tool, the WGA function provides a highly accurate and quick alignment of large genomes even with Indel containing data sets and for the first time ever, Roche 454 system reads. The whole genome view uniquely presents annotation information on a single screen, instantly providing researchers with a wide array of knowledge.”

NextGENe includes completely annotated references of the Human, Rat and Mouse genomes and also includes a special tool for the creation of additional reference genomes by the user.

Technical details of the NextGENe Whole Genome Alignment methodology as well as complete information on NextGENe, and a free 30-day trial request form is available on the company’s website: or by email:
Attached Files
File Type: pdf GenomeAlignment_NextGENe_AppNote.pdf (2.14 MB, 22 views)
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