PLOTREP: A tool for
visual analysis of dispersed genomic repeats
Aim
PLOTREP is
designed to be used by anyone who would like to identify
interspersed repetitive elements in BAC-sized or smaller
genomic regions. PLOTREP can merge fragments belonging to
the same copy of a repeat and allows rapid visual inspection
of the results via a dot-plot like two-dimensional graphical
output.
Overview
Identification of dispersed repeats, most
of which are derived from transposons and retrotransposons,
is an important step in genome annotation. Software tools
that compare genomic sequences to precompiled repeat
reference libraries using sensitive similarity-based methods
provide reliable means of finding the positions of fragments
homologous to known repeats. However, their output is often
incomplete and fragmented due to the mutational processes
(nucleotide substitutions, extensive deletions or
insertions) that can result in considerable divergence from
the reference sequence. Merging these fragments to identify
the whole region that represents a fossilic copy of a mobile
element is challenging, particularly if the element is large
and suffered multiple deletions or insertions of younger
transposable elements.
Using the PLOTREP web tool, repeats can be
identified in BAC-sized genomic regions (up to several
hundred kilobase pairs). First, a sequence similarity search is
carried out to detect matches against a library of various
reference sequences. The user can also compile and upload
his/her own set of known repetitive sequences to be used as
the reference library.
Positions of matching fragments in the genomic query are
determined using CENSOR (Jurka et al. 1996) in the searching
step. Results are then plotted as a two-dimensional dot-plot
like representation of sequence similarity. All fragments
predicted to be parts of the same original copy of a repeat
are merged and plotted to show the whole region covered by
the element. Positions of large deletions and insertions
with respect to the reference sequence are listed in the
output. Further analysis of sequences causing insertions of
more than a few hundred base pairs may reveal previously
unknown families of mobile genetic elements.
Click
here to submit a search. A standalone version of the
program for merging and plotting repeats is available to the
academic community upon request from the authors.
Note
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