Software
The electronic data files for sequencing are sent in a .seq or an .ab1 file. The .seq file is merely a text file that most use for blasting into available databases. The .ab1 file is the Applied Biosystems electropherogram (chromatogram) type file that is generated using ABI’s Sequencing Analysis Software that analyzes data generated by the 3730’s Data Collection Software. There are many downstream applications that are available for use in the manipulation of the generated sequencing files. The MBRF has purchased 6 licenses (4 for PC, and 2 for Mac operating systems) from GeneCodes called Sequencher 4.5. It is a powerful program that allows you to view, edit, and contig various sequencing sample results files. It produces consensus sequences, as well as finds specific areas that you define along with various restriction sites that you may wish to use. We keep the Sequencher software available for installation on your personal or laboratory computers. Arrangements can be made for you to come by the lab and take the software installation discs back with you for installation.
The Genescan Analysis software supplied by ABI for the 3100 is used to rapidly analyze your sample and produces .FSA files for your downstream applications. The settings for the analysis of each run can be manipulated to maximize the data accuracy and remove any ambiguous noise that may be present from low signal samples. The lab manager will teach and advise on how to further improve the results by manipulating the software and running modules, as well as be able to advise clients on how to proceed.
ABI has some freeware available called Peak Scanner Software v1.0. It will allow you to view, evaluate, and modify your .FSA files created using the ABI 3100’s data collection software. You may find that you like it better than the Lab’s Genescan Analysis software. They both perform the same functions however.