Gene Codes Corporation

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Gene Codes Corporation
Company typePrivately held
IndustryBioinformatics and Engineering
HeadquartersAnn Arbor, MI, USA
Key people
Howard Cash
President and CEO[1]
ProductsDNA Sequence Analysis Tools

Gene Codes Corporation is a privately owned international firm based in Ann Arbor, Michigan, which specializes in bioinformatics software for genetic sequence analysis. Its flagship software product, Sequencher, is a sequencing software used throughout the world. Its targeted use is by researchers at academic and government labs as well as biotechnology and pharmaceutical companies for DNA sequence assembly.


Gene Codes Corporation was founded in 1988 in Ann Arbor, Michigan. In 1991, the DNA sequence assembly and analysis software, Sequencher, was released. By 1997, nearly every major pharmaceutical company and commercial genomics company in the world was standardized on Sequencher, as well as the majority of labs at major academic centers. Sequencher 5.4 was released in 2015.[2]


Sequencher 5.1 has the ability to perform Sanger Sequencing and Next Generation Sequencing. It has advanced tools that aid in the general analysis of sequences and create reports that are an in depth analysis within customer data set.

General Analysis
  • Reference sequence alignment
  • Variance Table
  • Extensive import and export capabilities
  • NCBI BLAST Search
Sanger Sequencing
  • Import data from any of the major CE instruments
  • Clean up raw data by trimming vectors low quality bases
  • Perform alignment de novo or reference based assembly with flexible
  • Move easily between aligned data files analyze traces locally or globally to find secondary or uncalled peaks.
  • Instantly move between raw sequence multi-frame translation and restriction maps
  • Set up reusable templates for common projects letting you use base numbering and features from the reference sequence to annotate new alignments
  • Compare similar projects using a variance table
  • Advanced powerful tools to detect mutations and SNPs and refer back to raw data to eliminate sequencing artifacts
  • Generate reports that quickly and clearly document research findings
Next-Generation Sequencing
  • Easily import NGS reads
  • Choose either Maq or GSNAP as your alignment algorithm
  • View results using Tablet
  • SNP analysis and Methylation studies


  • The International Society for Computational Biology recognizes Howard Cash and Gene Codes Forensics for the unique application of computational biology to help with disaster victim identification. ISCB President Michael Gribskov called Gene Codes' contribution "unique, valuable, and beyond the limit of what could be expected".
  • Ann Arbor IT Zone recognizes Gene Codes Corporation with the Indestructible Award for Growth and Achievement.
  • Gene Codes is awarded the Merlanti Prize for Best Practices in Business Ethics.
  • Genome Technology makes Howard Cash Person of the Year in their All-Star Awards.
  • Gene Codes Corporation is named one of the Future 50 of Greater Detroit: "In recognition of your outstanding contribution to Metropolitan Detroit through sales and employment growth."
  • Ernst & Young and The New Enterprise Forum name Howard Cash, President, CEO and founder of Gene Codes, Entrepreneur of the Year.
  • Gene Codes wins the Washtenaw County Fast Track Award.
  • Sequencher receives the Best DNA Sequence Assembly Product from the Biotechnology Software & Internet Journal.
  • Gene Codes receives Michigan Leading Edge Technology Award in the biotechnology category. The award recognizes innovations introduced with Sequencher version 3.0, giving special mention to enhancements that allowed increased process automation.
  • Gene Codes receives the Best Presentation of the Year award by the Michigan Branch of the New Enterprise Forum: "In recognition of an innovative business venture which has helped make Gene Codes Corporation a model entrepreneurial firm."


  1. ^ Gene Codes Appreciation Page, Jonathan Hoyle's Web Site
  2. ^ Gene Codes Releases Sequencher 5.4, DNA Sequence Analysis Software, November 10, 2015 10:00 AM Eastern Standard Time, BUSINESS WIRE
  • Thomas D. Wu and Serban Nacu, Fast and SNP-tolerant detection of complex variants and splicing in short reads, Bioinformatics 2010 26: 873-881
  • Heng Li, Jue Ruan and Richard Durbin, Mapping short DNA sequencing reads and calling variants using mapping quality scores, Genome Research 2008 18:1851-1858
  • Ian Milne, Micha Bayer, Linda Cardle, Paul Shaw, Gordon Stephen, Frank Wright and David Marshall, Tablet next generation sequence assembly visualization, BioInformatics 2010 26: 40-402

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