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Evaluating and Editing Sequence Results

Instructions

Sequence calls by the analysis software can have several types of problems, and we recommend that all users evaluate and edit the automated sequence calls as necessary by examining the actual color peak data in the chromatograms. The areas that you should pay particular attention to are:

  1. Errors in base calls at the start of the sequence due to noise.  You may decide to trim away some of the beginning sequence to avoid these error.

  2. Occasional bases missed in the first 80 bases due to compression.

  3. Possible miscalled bases in areas where signal may be low.

  4. Incorrect base calls beyond 600 bases where resolution is deteriorating.

  5. Determining where usable sequence stops, and trimming the remaining base calls.

Two programs are available for viewing and editing chromatograms on a Mac: EditView and Sequencher. EditView allows opening, editing, exporting, and printing of one sequence file at a time. It is self explanatory, and easy to use. You can download EditView from Applied Biosystems web site.
Sequencher is a  commercial software by GeneCodes. The network versions of Sequencher together with Mac Vector, and  Vector NTI are maintained on the key servers of the Penn Bioinformatics Core for use by the facility users. Please contact the Bioinformatics Core to get access to this software package. Sequencher is a sophisticated, commercial software for sequence editing and assembly. DNA Sequencing Facility offers training on how to use Sequencher.

Applied Biosystems has a software for PC users, Sequence Scanner. The free Sequence Scanner Software enables you to view, edit, print and export sequence data generated using the Applied Biosystems sequencers. The software generates graphically expressive reports on results.
The PC users can also  download freeware for viewing chromatograms. Two such programs are –
Chromas 
Trev: available via FTP