Software - TRFragCalc

The free MATLAB script available on this page can only run with MATLAB already installed on your system (Windows, Linux, and MacOS). Please visit MATLAB to get more information about the purchase and installation.
TRFragCalc - in silico prediction of terminal restriction fragments

The script TRFragCalc was written in MATLAB (v. R2009b, MATLAB The Language of Technical Computing, The MathWorks, Natick, USA) to perform in silico a terminal restriction fragment length polymorphism (T-RFLP) analysis of 16S rRNA gene sequences. For more information on T-RFLP, please read Liu et al. (1997). The sript provides an interactive procedure for a step by step analysis.
Before starting TRFragCalc (Step 0) the 16S rRNA gene sequences of the SILVA database need to be prepared in ARB (Ludwig et al. 2004).
Export all 16S rRNA gene sequences (which are of interest) that match with 0 to 2 mismatches the T-RFLP forward primer (e.g. 8-27F) and reverse primer (e.g. 907R). Truncate the sequences to the length specified by the forward and reverse primer using the editor in ARB.
The export from ARB and import into MATLAB of 16S rRNA gene sequences is via xml files. The data in the xml files are converted into a MATLAB structure formate (Step 1). Each xml file will be treated within the import procedure as seperated branch which allows during the analysis to differentiate between bacterial groups (e.g. Alphaproteobacteria vs. Gammaproteobacteria).
To ensure that the results of the in silico digestion are comparable between the sequences TRFRagCalc prepares the sequences (Step 2) by (i) excluding sequences with ambiguities, (ii) excluding sequences that do not match the forward and reverse primer, and (iii) removing the 5' and 3' overhang.
For in silico T-RFLP analysis (Step 3) the skript provides the opportunities to determine (i) the length of the 16S rRNA gene sequences, (ii) the length of the in silico terminal restriction fragments (iTRF), and (iii) the G+C and A+G content of each sequence.
Finally (Step 4), the sript enables the possibility to search all 16S rRNA gene sequences that belong to a iTRF of specified length, or to determine the T-RFLP pattern of a bacterial group.

The zipped folder TRFragCalc_v_1.1 includes the files of the MATLAB script.
The zipped folder SILVA_rel102_827F_907R_2MM includes xml files which represent the prepared database of 16S rRNA gene sequences of all bacterial phyla.

Last updated: R.L. Hahnke, 20 August 2013
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