packFinder: packFinder: a package for the de novo Annotation of Pack-TYPE...
In packFinder: de novo Annotation of Pack-TYPE Transposable Elements
Description
Main Algorithm
Workflow
Author(s)
See Also
Description
Algorithm and tools for in silico pack-TYPE transposon
discovery. Filters a given genome for properties unique
to DNA transposons and provides tools for the
investigation of returned matches.
Main Algorithm
The goal of packFinder was to implement a simple
tool for the prediction of potential Pack-TYPE
elements. packFinder uses the following prior
knowledge, provided by the user, to detect transposons:
Terminal Inverted Repeat (TIR) Base Sequence
Length of Terminal Site Duplication (TSD)
Length of the Transposon
These features provide enough information to detect
autonomous and pack-TYPE elements. For a transposon
to be predicted by packFinder its TSD sequences
must be identical to each other, its forward TIR
sequence must match the base sequence provided and
its reverse TIR sequence must match its reverse complement.
Transposons are therefore predicted by searching a
given genome for these characteristics, and further
analysis steps can reveal the nature of these elements
- while the packFinder tool is sensitive for the
detection of transposons, it does not discriminate
between autonomous and Pack-TYPE elements. Autonomous
elements will contain a transposase gene within the
terminal inverted repeats and tend to be larger than
their Pack-TYPE counterparts; pack-TYPE elements
instead capture sections of host genomes. Following
cluster analysis, BLAST can be used to discern
which predicted elements are autonomous
(transposase-containing) and with are true
Pack-TYPE elements.
Workflow
An example of a standard workflow can be found using
browseVignettes(package = "packFinder"). The
primary functions include:
packSearch - the packSearch algorithm
uses simple pattern matching to detect
DNA transposons.
packClust - VSEARCH is used for
clustering elements based on sequence
similarity.
Having obtained the sequences of transposable
elements in a given genome, it is recommende
to carry out a BLAST search for each transposon
cluster. This can identify which elements are
likely autonomous, and which may be Pack-TYPE.
The packFinder functions report the
position of elements in a given genome using a
dataframe in the format of packMatches.
This dataframe is in the format produced by
coercing a link[GenomicRanges:GRanges-class]{GRanges}
object to a dataframe: data.frame(GRanges).
Author(s)
Jack Gisby
See Also
packFinder documentation built on Nov. 8, 2020, 5:24 p.m.
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Description Main Algorithm Workflow Author(s) See Also
Description
Algorithm and tools for in silico pack-TYPE transposon discovery. Filters a given genome for properties unique to DNA transposons and provides tools for the investigation of returned matches.
Main Algorithm
The goal of packFinder was to implement a simple tool for the prediction of potential Pack-TYPE elements. packFinder uses the following prior knowledge, provided by the user, to detect transposons:
Terminal Inverted Repeat (TIR) Base Sequence
Length of Terminal Site Duplication (TSD)
Length of the Transposon
These features provide enough information to detect autonomous and pack-TYPE elements. For a transposon to be predicted by packFinder its TSD sequences must be identical to each other, its forward TIR sequence must match the base sequence provided and its reverse TIR sequence must match its reverse complement.
Transposons are therefore predicted by searching a given genome for these characteristics, and further analysis steps can reveal the nature of these elements - while the packFinder tool is sensitive for the detection of transposons, it does not discriminate between autonomous and Pack-TYPE elements. Autonomous elements will contain a transposase gene within the terminal inverted repeats and tend to be larger than their Pack-TYPE counterparts; pack-TYPE elements instead capture sections of host genomes. Following cluster analysis, BLAST can be used to discern which predicted elements are autonomous (transposase-containing) and with are true Pack-TYPE elements.
Workflow
An example of a standard workflow can be found using
browseVignettes(package = "packFinder"). The
primary functions include:
packSearch - the packSearch algorithm uses simple pattern matching to detect DNA transposons.
packClust - VSEARCH is used for clustering elements based on sequence similarity.
Having obtained the sequences of transposable elements in a given genome, it is recommende to carry out a BLAST search for each transposon cluster. This can identify which elements are likely autonomous, and which may be Pack-TYPE.
The packFinder functions report the
position of elements in a given genome using a
dataframe in the format of packMatches.
This dataframe is in the format produced by
coercing a link[GenomicRanges:GRanges-class]{GRanges}
object to a dataframe: data.frame(GRanges).
Author(s)
Jack Gisby
See Also
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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