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FragMatch |
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Overview:
This program is designed to match sample (=unidentified) DNA fragment patterns to known patterns for reference species/individuals. FragMatch has been developed to overcome some of the limitations of previous programs designed for this purpose. Fragmatch can analyse DNA fragment data produced using a range of molecular approaches commonly used in mycorrhizal ecology including T-RFLP, microsatellite PCR etc. DNA fragment values from sample files are compared against a set of reference fragments for known species/individuals. For example, T-RFLP fragment patterns derived from ectomycorrhizal fungal communities (tips or soil) can be compared against a set of reference fragment patterns derived from identified fruit bodies, or ectomycorrhizal root tips providing a means for species identification.
As output, the program reports all full matches found within a sample file (i.e. the reference species for which all reference fragments were found within the set error limits in the sample file). If no full matches are found, a number (determined using the settings option) of close matches are shown. The output can be viewed in two different formats. The detailed view reports, for each full/partial match, the matched reference fragments along with the found match from the sample. This form of output also includes other information, such as the error limits used, any weighting used and the date and time of the analysis. Alternatively, an overview of the results can be viewed. The overview shows a column of all the sample files analysed on the left and each subsequent column to the right represents the individuals in the reference set. For each sample, the number of reference fragments detected per reference unit is shown (e.g. 1_4, means that a match has been detected for 1 out of a possible 4 fragments for the reference unit).
The program accepts sample files in Tab delimited text file format (*.txt). Fragment data from ABI sequence analysis software can be directly exported in this format, although it may be necessary to combine/modify files in Notepad or Microsoft Excel.
