Downloadable FireSat algorithm implementations
The Octave/Matlab versions of FireSat implement functionality to find TRs of lengths 10 to 200. Three versions are provided. However only the final version has been more fully analysed and optimized for accuracy using an ROC analysis. Provided demo data has TRs at every 1000 nucleotides.
The main file is: "/phd_cdr_implement/firesat_3/15_fsat/latest/try_do_find_trs_110_default.m".
Parameters are currently set to default but can be tweaked by editing them in the preampble of this file using either Matlab or Octave. The current run time for this example in Octave is 26s and on Matlab 2.6s on a Dell Precision laptop with an 6th generation i7 processor.
An alternative main file, prompting the user to select files from provided input data sets, can be found in the downloaded zip at: "/phd_cdr_implement/firesat_3/15_fsat/latest/find_trs_user_input.m".
The advanced commandline version runs on Windows and Linux. It has added functionality including that it finds TRs of length 1 to 6. One can add TranscriptInfo as parameter and can only partially parse an input file if one so wishes. A batch file is included in th zip as an example of usage.
FireSat was tested on Octave version 4.2.1 and on Matlab version 2016b both 64bit and runs on Windows 7 or later.
The absolute substring version runs on Windows and was implemented by calculating thresholds based on the absolute substring error as defined in this document.
The relative substring error version runs on Windows and was implemented by calculating thresholds based on the relative substring error. The relative substring error is defined as the substring error here and here.
The FireµSat2 ReadMe file provides instructions for the installation and execution of the FireµSat2-GUI version as well as an explanation of the options to execute the command line version.
The FireµSat2 Input/Output document provides a description of the usage and range for the input parameters of FireµSat2. A discussion of the output format of FireµSat2 is also included (applicable to all versions).
- Results of the verification of a published comparative study on PTR detection
The following table presents the scripts used to verify the results of 3 packages when searching for PTRs on the specified dataset as published in the article titled Review of tandem repeat search tools: a systematic approach to evaluating algorithmic performance in the journal Briefings in Bioinformatics.
|ptrfind.m||none needed||none||none needed||596 PTRs len>=20|
|FireµSat2||runall6err0_no_trinfo_20.bat||article_seq_20.zip||try_firemusat.m||596 PTRs detected|
|T-Reks on 24 Sept '12||sim=1.0, overlaps=OFF,indels=0%||t_reksm.zip||try_treks.m||393 PTRs detected|
|INVERTER on 24 Sept '12||Min-len=20, Subset=ON||inverter_new.csv||try_inverter.m||125 PTRs detected|