we first prepared a query library by clustering the 165 RT amino acid sequences of Gypsy and Copia reference elements taken from Gypsy database version 2 (Llorens et al., 2011) at a depth of 40% ident
This archive contains the main output files obtained with CAULIFINDER Branch A on the Vitis vinifera genome using default settings and default libraries (run 1 )
This archive contains, for each cluster of plant-derived genes, the initial (.aln files) and trimmed (.trim files) protein alignments in fasta format, and the phylogenetic trees in Newick format (.ann
We detected a protein domain with similarity to 2-oxoglutarate/Fe(II)-dependent dioxygenases (2-ODDs) superfamily (cl/PFAM13532) in 38 and 23 consensus sequences established from the genome of the orc
