Softgenetics - Software Power Tools for Genetic Analysis

GeneMarker® is unique genotyping software with application oriented defaults that dramatically reduce analysis set-up time. Analysis is typically 3-clicks away from completion…PARAMETER SETTING…DATA SIZING…ANALYSIS REVIEW. The software’s robust sizing and pattern recognition technology automatically remove chemistry and separation artifacts.

Medical researchers, pathologists or cytogenetic groups benefit greatly from the integrated MLPA, MS-MLPA, Trisomy, or LOH analysis modules that reduce error-prone, and time consuming data transfer by integrating the complete analysis from data sizing through patient reporting.

GeneMarker’s unique technologies have made it the software of choice of researchers performing AFLP, t-RFLP, Microsatellite, SBE, Cluster Analysis, SnapShot®, SNPlex®, SNPWave® or any fragment analysis the world over.

GeneMarker has been designed to provide genetic researchers with a biologist friendly genotyping 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 slab gel image files (TIFF,BIP,JPEG and TXT) from such systems as the LI-COR DNA Analyzers and Kodak Image Station when used in combination with JelMarker.

GeneMarker is a replacement for such software packages as SAGA from LI-COR, TrueAllele from Cybergenetics, GeneMapper, Genotyper, and GeneScan from Applied Biosystems, MegaBACE Genetic Profiler and Fragment Profiler software.

The basic operation of GeneMarker automatically corrects for most instrument and chemistry errors, such as saturated peaks, noisy data, wavelength bleed-through, instrument spikes, and stutter peaks. GeneMarker’s automated Run Wizard is designed to make repetitive 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 automatically performs 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.

Application Notes

Clustering Algorithms for Genetic Analysis with GeneMarker® Note [PDF]
Analysis of MegaBACE™ Data with GeneMarker® Software Application Note [PDF]
Capillary Tilling Application Note [PDF]