identifyTirMatches: Identify Terminal Inverted Repeat Matches

In jackgisby/packFinder: de novo Annotation of Pack-TYPE Transposable Elements

Identify Terminal Inverted Repeat Matches

Description

Searches a DNAStringSet for potential TIRs based on sequence similarity.

Usage

identifyTirMatches(
  tirSeq,
  Genome,
  mismatch = 0,
  strand = "*",
  tsdLength,
  fixed = TRUE
)

Arguments

tirSeq	A DNAString object to be searched for.
Genome	A DNAStringSet object containing the DNAString objects to be searched.
mismatch	The allowable mismatch between tirSeq and a given slice of Genome. Includes indels.
strand	The directionality of the search string ("+" or "-"). Note that this does affect the search for tirSeqs, if you wish to search the reverse strand you should use the reverse complement of your sequence.
tsdLength	Integer referring to the length of the flanking TSD region.
fixed	Logical that will be passed to the 'fixed' argument of matchPattern. Determines the behaviour of IUPAC ambiguity codes when searching for TIR sequences.

Details

Called by packSearch. Used by packSearch as an initial filtering stage. matchPattern from Biostrings is used for pattern matching. It is recommended to use the general pipeline function packSearch for identification of potential pack elements, however each stage may be called individually.

Value

A dataframe, tirMatches, containing identified matches. The dataframe is in the format generated by packSearch.

Author(s)

Jack Gisby

See Also

DNAStringSet, packSearch, matchPattern, DNAString

Examples

data(arabidopsisThalianaRefseq)

forwardMatches <- identifyTirMatches(
    Biostrings::DNAString("CACTACAA"),
    arabidopsisThalianaRefseq,
    tsdLength = 3,
    strand = "+"
)

jackgisby/packFinder documentation built on July 19, 2022, 2:25 a.m.