Uses hits, previously generated using blast, to annotate transposon hits. Transposons with non-redundant transposase hits are classed as autonomous ("auto"), while others are classed as "other" or "pack" based on whether the element has non-redundant hits to other proteins.
blastAnnotate(protHits, autoHits, packMatches)
BLAST results for non-transposon related genes or
proteins (as a
BLAST results for transposon related genes or
proteins (as a
A dataframe of potential Pack-TYPE transposable elements,
in the format given by
Returns the original
with the addition of a "classification" column
containing one of the following values:
auto - elements that match known transposases or transposon-related proteins are classified as autonomous elements
pack - elements that match other proteins or genic sequences may be classified as Pack-TYPE elements
other - elements that generate no significant hits
Requires that the query ids in the protein and autonomous hits match the row names in packMatches.
For further information, see the NCBI BLAST+ application documentation and help pages (https://www.ncbi.nlm.nih.gov/pubmed/20003500?dopt=Citation).
data("packMatches") # read in some protein hits p <- data.frame( query_id = c(2, 3), subject_id = c("prot", "hyp") ) # read in some autonomous hits a <- data.frame( query_id = c(3, 4), subject_id = c("transposase", "mutator") ) blastAnnotate(p, a, packMatches)
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