Alternative methods for viewing sequence chromatograms:

• Through LaserGene.  LaserGene can be run from your PC on the Bioinformatics core site license.  The general procedure is:
• Save your .ab1 files to your computer.  Avoid saving from webmail; use Eudora or other mail program.
• You must get a username and password for accessing LaserGene through the site license.  Contact Dr. Demeler or Jeremy Mann.
• Your PC must be set up to access the University Microsoft NT domain.  From outside the UTHSCSA domain you must have installed a vpn connection, and activate that first.
• In the <Start><run> box type //129.111.69.180, and enter your username and password for LaserGene when prompted. (For some of the older windows systems, it will use your desktop username and password automatically, so you may have to create a user by that description and login to the PC as such).
• Click the DNAStar folder in the window that opens.
• Click the SeqMan folder.
• Click the SeqMan.exe file.
• Click on <file><new>
• Click <skip> on the window asking about vector data.
• Click <add sequences> on the "unassembled sequences window"
• Navigate to folder with ab1 files, select one or more, click <add>, and <done>.
• Select a sequence to view from menu and click <sequence><show trace data>
• Through Vector NTI.
• Vector NTI is available through the Bioinformatics Core on a site licesnse for both PC and Mac OsX..
• The first time you use Vector NTI on a particular computer on the University site license, there is is a lengthy download process.  Get authorization from Dr. Demeler or Jeremy Mann, and see the installation notes on the bioinformatics web site.
• When you use Vector NTI, you must request one of the slots available under the site license for the particular program you want to use.  In this case, run the License Manager (<Start><Programs><Informax><License Manager>), and set the Contig Express Box to <Dynamic License>.  The first time you request a license slot there are extra steps to fill out some forms.  These steps are also described at the bioinformatics web site.
• Now Run the Vector NTI contig express program (<start><programs><Informax><Vector NTI suite 8><Contig Express>).
• Under the <project> menu click on <Add fragments> and <from ABI files>
• Navigate to your directory with the ab1 sequence(s) and load one or more sequences.
• Double click on the .ab1 file you wish to view in the resulting menu.
• Your slot to use this program will expire in a week, at which time you will have to renew it.  If you will not use it again soon, please use the License Manager and set Contig Express back to "Demo" so that you will not tie the slot up for someone else who wishes to use the program.
• The Core facility uses Sequencher.  There is a copy installed for users in the facility that works in demo mode.  You could view your data there, but not save or print it.
• The Core facility recommends installing the following software to view chromatograms:
• For Macs: EditView from Applied Biosystems.
• For PC's: Chromas from www.technelysium.com/au/chromas.html.
• EMBOSS abiview accessed at the bioinformatics core.  This program could not scroll through the chromatogram, so it was not particularly helpful for normal use.  However, for the purpose of printing color chromatograms, its cps option was excellent.
• The chromatograms can be viewed on software native to the sequencers themselves prior to being exported for analysis.  This means of viewing the sequence is generally only open to the facility operators.
• The Phred/Phrap/Consed system available through the bioinformatics core facility is generally only used for large shotgun assembly projects.  We currently don't have a help file describing all the steps necessary to set up a new user.  You would have to consult the Bioinformatics core or Dr. Hardies if you wish to use this system.  Chromatograms are viewed in context with assembled sequence through Consed. This system makes it generally difficult to view the chromatogram of a sequence prior to assembly.  Basically one has to create a dummy database and force the sequence reads into it.