There are several different options for users to view and analyze their DNA sequence data. GNomEx, our online sample tracking system, provides a few options for reviewing the sequences. If you need to align data or build contigs you will need a third party software application.

Sequencing Software

Sequencher, from GeneCodes, is a software application you can use to review, edit and align your sequences. The latest version of the software (v.5.3) also allows you to align against a true reference and generate a variance or mutation report. We recommend the use of Sequencher.

The Core Lab maintains 11 network licenses of Sequencher, 6 for Macs and 5 for PCs, available to users. Effective September 1, 2010 we will charge a $1 per use fee for each hour of use when you log in to Sequencher. The reason we are charging per hour, is that users log in and forget to log out, thereby tying up a license. By charging $1 per use up to an hour, we hope to discourage users simply logging in to capture a license and then never logging out.

Users who submit sequences to our Core will be rebated the $1 usage fee, as the cost of Sequencher access will be subtracted from their sequencing bill. Most sequencing users will not pay any more for Sequencher access because we will recoup some of the cost of Sequencher from the users that do not use our DNA Sequencing Facility.

Pathology Users: Your department has a version of Key Server running, so you cannot log in to ours and use our Sequencher Licenses. Your department has Sequencher Licenses for use on your network. These can be accessed by calling Pathology IT. We apologize for any inconvenience.

OFF CAMPUS Users: The key server cannot be accessed from off campus unless you are using a VPN. If you have questions on this, call Derek at (801)-581-4736.
To be able to use our network license of Sequencher you need to:

  1. Have an active account with the Core facility and be a sequencing customer
  2. Download the appropriate version of Sequencher for your computer.
  3. Install the Key Access software first (it downloaded in the same .zip file as Sequencher)
  4. Add the IP address below to the Key Access software.
  5. Place the downloaded .lic file into a folder where you’ll know where to find it. (I often suggest making a “Licenses Files” folder in your “Documents” and putting it there)
  6. Install Sequencher. (When asked for a license, click “I already have one” and point it at the .lic file you just saved)
  7. If you haven’t configured the Key Access software correctly, Sequencher will run on “demo mode” and you will not be able to save, print or export your project.

The KeyAccess IP address is: 155.101.153.88 both for Macs and PCs.
KeyAccess will request your login name and password. This is currently a separate system from GNomEx, but we hope to eventually link the two.

How to change the IP address for KeyAccess:
  • PC users: Go to Start menu > Control Panel > KeyAccess. Change the IP to: 155.101.153.88
  • Mac users: Go to System Preferences > Other: KeyAccess, and change to the same IP above
Sequencher Downloads:

 

PLATFORM PC MACINTOSH
System Requirements Windows XP, 7, 8.1 OS 10.3.9 or higher OS 9.2 or OS 10.2 to 10.7 OS 8.6 or higher
Sequencher Version 5.4.1 5.4.1 4.5 4.2
Network Available Licenses 5 6 6 6
Download Download Download Download

Notes on Sequencher Usage:

  • Please safeguard your login name and password!  PIs and lab managers, please contact us about people that are no longer in your lab so we can deactivate their online accounts.
  • Technical Support from GeneCodes is available to all Core users: (800) 497-4939.
  • Mac users: when you are done using Sequencher, make sure you’ve quit the program, not just closed the project window. If the program is on, you are in fact holding up a network license and keeping somebody else from using it (and costing your lab money)!

Benefits of the Core Facility Sequencher Network Licenses:

  1. You’ll have access to the latest version of Sequencher, which is one of the best and easiest software packages to use for Sequencing analysis.
  2. You can install the program on as many computers as you wish on campus.  Off campus may be possible with some effort.   Contact the core if this is necessary.
  3. You will have access to the GeneCodes customer support if you have questions on how to use Sequencher.

The Core is happy to help you learn Sequencher. Please call us at (801)-585-2976 if you need help on this.

Other Analysis Software for DNA Squence

PC users:

Mac users

Primer Customization Software

Primer3 is a widely used primer customization packaged available through either a web interface or downloadable source code. We recommend Primer3 as an excellent starting point for developing your own custom primers. General information about the history and capabilities of Primer3 are available here.