Examples :
VNTRfinder and PolyPredictR
Comparison of two bacterial sequences – Neisseria
meningitides MC58 vs. Z2491
Test and results files used in the original
publication
If you
would like to see further examples, please suggest these to vntrfinder@gmail.com
See also the documentation and download the tutorial.
The size of your sequence(s)
will determine the length of time a search will take, as will specifying a high
maximum mismatch tolerance for the flanks. This is because the VNTRfinder
program will repeat a search for homology until the maximum mismatch value has
been reached before moving on to the next repeat. Also, choosing parameters for
the Tandem Repeats Finder program that identify more repeats will also increase
time as each repeat is searched.
Human vs. Orangutan
occludin
Enter human as the reference
Enter orangutan as the target
Specify
Tandem repeats finder parameters: 20, 2, 7, 7, 500
Specify flanklength and mismatch parameters: 20, 5
Click on
“Search”
The visual
summary of your results will look like this:
Here are the
results of this search (tab delimited): (1) VNTRfinder output (2) PolyPredictR output
If you specified
the Tandem Repeats Finder parameters 50, 2, 7, 7, 500 you would get less
repeats and the results would look like this:
Here are the
results of this search (tab delimited): (1) VNTRfinder output (2) PolyPredictR output
è Note one less repeat in the second search.
Both these
searches take very little time.
Comparison of two
bacterial sequences – Neisseria meningitides MC58 vs. Z2491
Enter Neisseria meningitidis MC58
as the reference
Enter Neisseria meningitidis
Z2491 as the target
Specify Tandem repeats
finder parameters: 20, 2, 7, 7, 500
Specify flanklength
and mismatch parameters: 20, 5
(Note: This search can take a few minutes)
The visual summary of your
results will look like this:
Here are the results of this
search (tab delimited): (1) VNTRfinder output (2) PolyPredictR output
Tolerating no mismatches in
the flanks would give you this picture (less red meaning less repeats were
matched between the two bacterial sequences)
If you increase the flanklength to 40 and again tolerate no mismatches, you get
this:
If you specified the Tandem
Repeats Finder parameters 50, 2, 7, 7, 50 you would identify much fewer repeats
and the results would look like this:
Therefore, in the case of
bacterial sequence/genome comparisons, you should choose the types of
parameters that reflect the tandem repeats you are most interested in and/or
the required level of stringency in the search.
Test and results
files used in the original publication
Mycobacterium tuberculosis
Input files
Mycobacterium
tuberculosis CDC1551 (reference sequence)
Mycobacterium
tuberculosis H37Rv (target
sequence)
Results files
VNTRfinder results for repeats in CDC1551 searched against
H37Rv
PolyPredictR results for repeats in CDC1551
Neisseria meningitis
Input files
Neisseria
meningitis MC58 (reference sequence)
Neisseria
meningitis Z2491 (target sequence)
Results files
VNTRfinder results for repeats in MC58 searched against
Z2491
PolyPredictR results for repeats in MC58
If you would like to see further
examples, please suggest these to vntrfinder@gmail.com