This example is provided without underlying sequences database(s),
which has/have to be downloaded separately from the following links:

1. Ribosomal Database Project II at
   http://rdp.cme.msu.edu/misc/resources.jsp;jsessionid=81D78ABD098F7AF5EA2CC102FFAC0F4C

2. Greengenes at
   http://greengenes.lbl.gov/Download

3. ARB - silva at
   http://www.arb-silva.de/download

4. other potential resources

------------------------------------------------

You can run this analysis yourself by simple
modification of one line in BEsTRF parameter
file(s) of your choice as described below.

Other parameters are already set for ten
distinct analyses for you. Thus you have ten
distinct BEsTRF parameter files at hand that
differ in the number of allowed primer
mismatches (1mm, 2mm, 3mm), insertions and
deletions (Levenshtein (L111)) as well as
recognition of degenerated primer binding
sites (4MPD).

Therefore:

»0mm« in parameters' file names mean:
      no allowed mismatches

»1mm«, »2mm«, »3mm in parameters' file names mean:
      1, 2 or 3 allowed mismatches, respectively,

»4MPD« in parameters' file names mean:
       allow binding of primer to degenerated sites
       of any (up to level four) degeneracy,

»L111« in parameters' file names indicates usage
       of Levenshtein distance where mismatches,
       insertions and deletions all cost one quantum
       of penalty, and file name part »1mm«, »2mm«, »3mm«
       indicates total allowed mismatching cost.

------------------------------------------------

Create a new directory on your disc and unzip the
downloaded sequence database contents. The downloaded
database name should now read like the following,
depending on the database release:

release10_7_arch_aligned.fa

Optionally, you can rename the downloaded and unzipped
sequence database to a name of your preference. 

Open all or selected BEsTRF parameter files that are
provided for this demonstration in your preferred
text (ASCII) editor. The names of these files start
with params_....txt  . In the first line there is a
keyword "DNA_File_Names"  after which type in the
proper sequences input file name. The modified line
of BEsTRF parameter file should now read like this:

DNA_File_Names	release10_7_arch_aligned.fa

In case you decided to change the name of sequence
database to e.g. myBacteria.fa the line should read like this:

DNA_File_Names	myBacteria.fa


Now save the newly modified BEsTRF parameter file
(under the same name if you intend to run BEsTRF
through already prepared RunME_xxxxxxxx.bat files,
or alternatively you can save the file under new
name and fire up BEsTRF manually).

------------------------------------------------


Run demonstration(s) by double clicking on the
appropriate file(s) RunMe_xxxxxxxx.bat

Please read section 1.7 Computation time
on page 8 of Users’ manual.