Ann Arbor-based Gene Codes Corp. Monday released version 5.0 of its Sequencher biological research software.

The company says Sequencher 5.0 incorporates new DNA sequence data alignment algorithms with analysis of SNPs (a commonly found form of genetic variation in a DNA sequence) and methylation (a method to regulate the expression of genes) for next-generation DNA sequence data.

Performance for assembly and alignment of sequences and contigs (a set of overlapping DNA segments derived from a single genetic source) is hundreds of times faster. New alignment functions and database searching features make getting reliable results from both capillary electrophoresis and next-generation data faster than ever.

Gene Codes prioritized next-generation DNA analysis features for the Sequencher 5.0 release. It gives scientists an easy-to-use interface in the powerful, scientist-friendly tool that they are already comfortable with, while building the bridge to overcome the difficulty of using command-line driven algorithms.

“NextGen support in Sequencher builds on our tradition of expanding the software technology to meet the needs of our clients in the lab,” said Howard Cash, CEO of Gene Codes. “We are not introducing a new product for our client to buy in order to analyze their latest data. They’ve already made that investment. All of our current clients are receiving the upgrade to Sequencher 5.0 with NextGen support at no extra charge.”

Gene Codes plans to continue adding new functions from third parties, as Cash explained at the BIO 2011 International Convention in Washington D.C. Monday morning.

“Now that we have restructured the Sequencher architecture to put a graphic interface on algorithms and tools like Clustal, Maq, GSNAP and Tablet, we expect to release functionality for both Sanger and NGS data analysis at a fast rate,”  Cash said.

Sequencher 5.0 is capable of handling any traditional DNA data set from capillary electrophoresis machines and data from all of the major next-generation machines; Roche 454, Illumina, Life Technologies SOLiD, and Ion Torrent. Said Danielle Beekman at the University of Iowa: “We just installed Sequencher 5.0 and it was amazingly fast and easy for aligning sequences with GSNAP.”

GSNAP is an alignment algorithm which can detect complex variants and splicing in short reads. It was developed by Thomas Wu at Genentech and incorporated into this release of Sequencher. Said Wu: “Sequencher makes it easy for biologists to use GSNAP to align their sequencing reads, and provides an intuitive graphical interface for viewing the results.”

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