New DNA Sequence Analysis Software From Ann Arbor Firm

ANN ARBOR — Gene Codes Corp. announced the release of version 5.4 of its Sequencher DNA Sequence Analysis Software.

Sequencher 5.4 continues Gene Codes’ mission of empowering the bench scientist with the latest bioinformatics tools. Gene Codes has been developing Sequencher for more than 25 years with this goal in mind.

With new tools becoming increasingly more complex, Sequencher’s easy-to-use interface helps users spend more time in the lab instead of learning new software.

The new features in Sequencher 5.4 are aimed at improving the entire Next Generation Sequencing (NGS) analysis process from start to finish. With sequencing cores driving down the cost of obtaining NGS data, more and more users wanted a way to “look” at their raw data files to verify the quality. Sequencher’s answer to this is the addition of FastQC. Sequencher users can now generate an html report that gives them information on 11 different metrics of their raw NGS data, validating their lab work and saving time on wasted analyses.

Gene Codes has upgraded many of the RNA-Seq features that were added in Sequencher 5.3. The Cufflinks suite is a proven command-line driven RNA-Seq analysis tool, but it can be challenging to navigate through the multiple programs in the suite. Gene Codes offers its users customized graphic interfaces for each element that novice users can pick up in minutes.

Generating graphics to publish results often requires support from outside the lab. Sequencher 5.4 gives users an in-house solution. “Our clients are used to getting their results fast with an easy learning curve. We designed our RNA-Seq workflow and visualizations with that in mind. Using the enhanced Data Table, users can find and focus in on important data and export beautiful charts and plots in minutes,” said Howard Cash, President and CEO of Gene Codes.

Sequencher 5.4 users can now use SAMtools to call variants in their NGS alignments. The resulting variant calling file (vcf) can be imported alongside of the alignment into the Tablet viewer or other genome browsers. “Clients are always asking for more downstream analysis tools,” said Cash. “We want users to be able to stay in Sequencher and do the whole project from start to finish.”

Sequencher 5.4 is included as a free upgrade for clients enrolled in Gene Codes’ maintenance program. New users that want to take Sequencher 5.4 for a test drive can request a free fully-functional 30-day evaluation. For more information, visit or call (734) 769-7249.

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