blastAnnotate: Functional Annotation of PackTYPE Elements

View source: R/blastAnnotate.R

blastAnnotateR Documentation

Functional Annotation of PackTYPE Elements


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 data.frame). Generated using blastAnalysis.


BLAST results for transposon related genes or proteins (as a data.frame). Generated using blastAnalysis.


A dataframe of potential Pack-TYPE transposable elements, in the format given by packSearch. This dataframe is in the format produced by coercing a link[GenomicRanges:GRanges-class]{GRanges} object to a dataframe: data.frame(GRanges). Will be saved as a FASTA file for VSEARCH.


Returns the original packMatches dataframe, 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.


Jack Gisby


For further information, see the NCBI BLAST+ application documentation and help pages (

See Also

blastAnalysis, readBlast, packBlast



# 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)

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