HT Workflow

Scripts used in the discovery, curation and analysis of horizonally transferred repeats in Aipysurus laevis

Identification of repetitive sequences in Aipysurus laevis

Repetitive sequences identified and classified using CARP (Zeng et al. 2018)

transposon_finder.R - used to identify potential TEs from repetitive sequences identified by CARP based on protein domain presence

rpstblastn.sh - a shell script used to improve search speed for protein domains

solo_curator.R - used to curate potential transposons identified by transposon_finder.R

Presence/absence of highly similar LINEs in closely related species

Command line BLASTN+ (megablast) other snake genomes for HTT LINEs. Also used to identify to HTT LINEs in Aipysurus laevis transcriptome

Presence/absence and curation of similar LINEs other highly divergent taxa

repeatblaster.R - used to identify species containing repeats similar to the HTT LINES

extendAlign.R and variants - used to construct alignments of similar sequences found in each species. Alignments manually edited and consensus made in Geneious

Repeat phylogeny construction and figure building

lines_for_trees.R - used to identify intact LINEs from RepBase and consensus sequences based on protein domain presence

mafft used to align intact LINEs

Trimming of alignment - online Gblocks with "Allow smaller final blocks", "Allow gap positions within the final blocks" and "Allow less strict flanking positions"

raxml.sh - used for tree building

Repeat insertions near and in genes

overlapSearchConfirmations - used to identify insertions of HTT LINEs into near and into genes and confirm RepeatMasker annotation of said LINEs

insertionConfirmation.R - used to search for and create MSAs of ortholgous regions surrounding HTT LINEs inserted into and near genes in closely related species