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GeneMarker® for Fragment Analysis, Amplified Fragment Length Polymorphisms (AFLP), and Multiplex Ligation-dependent Probe Amplification (MLPA)

GeneMarker software has been designed and created in order to provide genetic researchers with a biologist friendly genotyping analysis tool. We incorporated the suggestions and requirements of several research groups into the software. Their main requirements were ease- of- use, high accuracy, flexibility and low acquisition cost.

GeneMarker can perform analysis on up to 1,000 lanes of four or five color data sets generated by either slab gel or capillary electrophoresis. It is a unique genotyping tool as it is compatible with files from all major capillary and slab gel electrophoresis systems including ABI files (*.FSA, .*AB1, *.ABI), SCF files, MegaBace files (*.RSD, *.ESD), SpectruMedix files (*.SMD, *.SMR), Beckman files, and Licor files. GeneMarker is a replacement for such software packages as SAGA from LI-COR, TrueAllele from Cybergenetics, GeneMapper, Genotyper, and GeneScan from Applied Biosystems.

GeneMarker is a single software package with applications for Fragment (microsatellite) Analysis with an integrated pedigree tool, Amplified Fragment Length Polymorphisms (AFLP), and Multiplex Ligation-dependent Probe Amplification (MLPA).

Additionally, the software automatically corrects for most instrument and chemistry errors, such as saturated peaks, noisy data, wavelength bleeding, instrument spikes, and stutter peaks. GeneMarker’s automated Run Wizard is designed to make analysis quick, easy, and accurate.

Nearly every function of GeneMarker has been automated so that once the template is selected from the menu, or created by the user, the software will automatically perform the analysis, providing a myriad of display and reporting options. Once the analysis has been completed and confirmed the software saves all of the analysis parameters, raw data and results for easy archiving and call back at a future date.

Simple, Easy Operation

Auto Run Wizard

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Once analysis parameters have been set or
saved, two mouse clicks, (data entry, and then
run) are all it takes to run an analysis on up to
1000 lanes of capillary data.

GeneMarker’s Run Wizard makes parameter
setting easy and straight forward. Previously
saved parameters can be applied to subsequent
analyses, increasing consistency while reducing
analyst set up time

Raw Data

Quality Control of Sizing

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GeneMarker provides a lane by lane overview
of unprocessed raw data, permitting a quick
quality control of the data.

GeneMarker provides a quality control graph indicating the linearity of the size call of each lane

Analysis parameter setting made easy

GeneMarker’s wizard simplifies parameter setting by “walking” the user through 3 simple steps. Templates can either be selected from several embedded templates or the user can create and save additional templates; detection settings are presented in one dialogue box that creates required flexibility in a simple to use format. Panel management and creation requires only a few mouse clicks! Once set the parameters can be saved and called back for future analysis.

Analysis Reporting



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Analysis results can be sorted and manipulated to
meet report requirements and then saved as a text file or input into LIMs or other data base systems.

GeneMarker will print reports of analysis for either all or selected sample sets. User can choose to include electropherograms, analysis text, and output sequence.


Copyright 2005. SoftGenetics, LLC. State College, PA USA 16803
Phone: 814-237-9340 Fax: 814-237-9343 Email: