FAQ:
VNTRfinder and PolyPredictR
What
if I don’t get a tandem repeat detected when I expect one?
What
if a repeat detected in the reference is not detected in the target sequences?
I’m
not sure how to fill in the query form, is there a tutorial?
How
long does a typical search take?
A
repeat I know to be polymorphic has not been predicted to be so?
If your
question(s) are not addressed here or in the documentation,
please send your query to vntrfinder@gmail.com
Two things:
Firstly, it
can predict potentially polymorphic repeats in one or more sequence (reference
sequence(s)). To only avail of this utility, enter sequences in the first
sequence box only.
Secondly, it
can search for repeat variation by aligning repeats from the reference
sequence(s) with repeats in one or more target sequence. To avail of this,
enter sequences in both the first and second sequence boxes.
Examples (Test1 and Test2) are available on the main search page. Also, examples
are presented and discussed on the examples page.
Try
lowering Tandem Repeats Finder’s parameters (lower minscore, mismatch or indel values).
(b) Try increasing the flanks a well
as the mismatch parameter:
The
VNTRfinder program automatically increases the
mismatch frequency (after starting at “0”) until it finds a match.
It may be that there are multiple possible matches, in which case the program
will not return a result, on the grounds that the mapping is ambiguous. The
positions of unambiguous matches detected are returned in the third output file
(“repeats detected in the reference(s) and found in the
target(s)”). In this case, edit down the query and target sequences to
restrict analysis to regions that exclude the ambiguities that you are certain
should not match; however, be careful that you understand the sequences are
truly homologous.
Secondly, the query form
allows you to choose one of four options in searching for matches across
sequences; (a) represents length difference consistent with change in the
repeat copy-number, (b) has the same repeat unit length and motif, (c) has any
repetitive sequence, (d) represents any sequence (i.e. no check). Choosing
option (a) instead of (d) will increase the stringency of the search for
homology and only matches for repeats that satisfy the criterion in question
will be reported, e.g. only matches containing the same tandem repeat unit and
motif.
There’s
a tutorial for internet explorer users at http://www.bioinformatics.rcsi.ie/vntrfinder/Tutorial.mht. Users of other browsers can download it at http://www.bioinformatics.rcsi.ie/vntrfinder/Tutorial.pps. Also, see the documentation at http://www.bioinformatics.rcsi.ie/vntrfinder/documentation.html.
If
you are comparing two genes of about 4kb each, the search will take about 5
seconds. The example files take less than 20 seconds. Genomes will clearly take
much longer and you are advised to download the programs and run these locally if running large
jobs. Also, a search can take a little longer than normal if you are searching
against more than one target sequence/genome.
The rules used by PolyPredictR to predict whether a repeat is polymorphic are
based on rules described in previous literature. As discussed in this
literature, there are rates of false positives. Also, the predictions are based
on repeats in human sequences and may not be applicable to all genomes.
If your question(s) are not addressed
here or in the documentation,
please send your query to vntrfinder@gmail.com