Databases

ROP uses the following reference databases:

• Ensembl GRCh37
• Human ribosomal DNA complete repeating unit
• RepBase20.07
• IMGT V(D)J genes of B and T cell receptors
• NCBI bacterial reference genomes
• NCBI viral reference genomes
• EuPathDB eukaryotic reference genomes
• Repeat annotations

Repeats

We use GTF files generated from the RepeatMasker annotations by Jin, Ying, et al. and downloaded from http://labshare.cshl.edu/shares/mhammelllab/www-data/TEToolkit/TE_GTF/. Repeat elements overlapping CDS regions are excluded from the analysis. We filtered out 6,873 repeat elements overlapping CDS regions.

Prepared repeat annotations (bed formatted file) are available at https://drive.google.com/file/d/0Bx1fyWeQo3cORi1UNWhxOW9kYUk/view?pref=2&pli=1. The prepared repeat annotations contain 8 Classes and 43 Families.