annotate_tir

find terminal inverted repeats (TIRs)

not worth removing terminal seq difference

Ac/Ds is terminated by imperfect TIRs, at the terminus.

cAGGGATGAAA tAGGGATGAAA

Kunze and Weil (2002), Mobile DNA II

Some TIRs can be short

Bergamo has 5 bp TIRs

CAGGG

Kunze and Weil (2002), Mobile DNA II

Rlibstree can be difficult to install, best way: install.packages("devtools") library(devtools) install_github("omegahat/Rlibstree")

path right now is: (need to clean up)

1. tir_search_simple.mismatchTIR.R - NOTE that this has to be on UNIX (even using R) because I'm having locale issues I haven't been able to resolve on my Mac.
2. add_families.R uses output from #1, but needs to be adapted to read in only gff's not the crazy large text file I output

This generates a gff3 with all TIR copies, not two (identical TIR and mismatch TIR) as I was doing before.

old path was (before Aug 29)

1. tir_search_simple.R
2. add_families.R not great documentation of how to get source
3. tir_search_simple.mismatchTIR.R - NOTE that this has to be on UNIX (even using R) because I'm having locale issues I haven't been able to resolve on my Mac.
4. add_families.mismatch.R uses output from #2