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Repeats treating software (alpha version)


This software (Repeats Treater) works with any size repeats sets allowing digrams construction of cleavage at certain recoginition sites (i.e. SE restriction endonucleases). 

Requirements:

Windows XP, Vista or Seven
1 Gb RAM (2 Gb - recommended)



This is early alpha version. Some restrictions apply:

support of FASTA formats only (.fasta and .txt file extensions)
only repeats treating is allowed (no genome treating, double digests etc.)
some optimizations are turned off
multicore/multiprocessor support is turned off
only 32-bit version
realtime diagrams viewing is turned off


Short help

 

  1. On the First Tab (File and Method) please click Browse button and choose the file with repeats set (you may use, for example, aligned set of human alu repeats). Only FASTA format is supported. Big files need some time to load. Feel free to make the next steps during the loading procedure.
  2. Change the name of the results file(s). The result will be saved as comma delimited files (supported by many popular editors and diagrams plotters). File name is constructed from this text fields and the name of restriction enzyme chosen for treating. Repeats treater creates 2 result files for each enzyme: small (useful for plotting the diagrams) ang big with full map (very useful for detailed study).
    You may leave this field unchanged but this alpha version does overwrite the files if they exist.
  3. Go to the Enzymes Tab and choose enzymes which recognition sites will be used for treating. Use multi-rules checkbox if you need to apply some basic group selections.
  4. Click Ok button to start the calculations.



Download Repeats Treater.