Key Features of GenoProfiler
 

Systems:

    • Java-based cross-platform software package for the fully automated processing of fingerprinting data.
    • GUI-based application running on any platforms supporting Java Virtual Machine (such as Windows, Linux, Solaris, Mac etc).

Inputs:

    • Supporting direct data reading from sample files of ABI 3100/3700.
    • Supporting size editing of fingerprinting profiles from ABI 3730 based on the outputs of GeneMapper (ABI).

Output:

    • Exporting edited size files compatible with FPC software.

Data Analysis and Tools:

    • Graphically viewing traces of sample files of ABI 3100/3700.
    • Automatically remove the background (noise) bands  and "false" bands in fingerprint profiles (based on built-in or user-defined cutoff values). 
    • Detecting and splitting double bands or triple bands.
    • Removing vector bands / repeat bands.
    • Fragment frequency analysis of edited fragment sizes.
    • Detecting and removing cross-contaminated clones within 384-well plates and 96-well plates and chloroplast-DNA-contaminated clones.
    • Renaming BAC clones based on actual clone names.
    • Removing substandard fingerprint profiles.
    • Sub-setting sample files from sample file directories.
    • Sub-setting clone names from contigs in fpc files (*.fpc).
    • Viewing fingerprint patterns.
    • Conversion between hybridization grid position and clone name (ID).
    • Conversion to Ace file format from clone-marker hybridization data.

References

  1. You, F. M. and Luo, M.-C, 2003. GenoProfiler User's Manual. http://wheat.pw.usda.gov/PhysicalMapping/tools/genoprofiler/manual/.
  2. You FM, Luo MC, Gu YQ, Lazo GR, Deal K, Dvorak J, Anderson OD. 2007. GenoProfiler: batch processing of high-throughput capillary fingerprinting data. Bioinformatics. 5;23(2):240-2. Epub 2006 Oct 2.