identifyTirMatches: Identify Terminal Inverted Repeat Matches
In packFinder: de novo Annotation of Pack-TYPE Transposable Elements

Description Usage Arguments Details Value Author(s) See Also Examples

Searches a DNAStringSet for potential TIRs based on sequence similarity.

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

`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.

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.

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

Jack Gisby

DNAStringSet, packSearch, matchPattern, DNAString

data(arabidopsisThalianaRefseq)

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