Generating a BioMart Other RNA annotations BBMap database

This page describes how to generate an annotations database containing “Other RNAs” such as snoRNAs and lncRNAs.

If you do not wish to supply a real BioMart file, simply download and point Prost! at the following fake BioMart file: fake_biomart_file.fa

Download the sequences from BioMart

  • Open http://ensembl.org/biomart in your browser.

  • Make the following selections:

    • Click - CHOOSE DATABASE - and select Ensembl Genes xx where xx is the current version of Ensembl.
    • Click - CHOOSE DATASET - and select your species of interest (e.g. Danio rerio genes (GRCz10)).
    • Click Filters
      • Click the + button next to GENE to expand that box.
      • Under Gene Type, select all of the following if present (you may have to ctrl-click or cmd-click to select multiples at the same time):
        • lincRNA
        • miRNA
        • misc_RNA
        • Mt_rRNA
        • Mt_tRNA
        • rRNA
        • snoRNA
        • snRNA
    • Click Attributes
      • Click the Sequences radio button.
      • Click the + button next to SEQUENCES to expand that box.
        • Click the cDNA sequences radio button.
      • Click the + button next to HEADER INFORMATION to expand that box.
        • Uncheck all the checkboxes.
        • Check the these boxes in the following order:
          • Gene Name
          • Transcript type
          • Transcript stable ID

  • Optional: Click Count to see how many sequences will be returned.

  • Click Results to generate the fasta file.

  • Click Go to download the fasta file containing the other RNAs.

  • Move the downloaded file (typically named mart_export.txt) somewhere appropriate on your computer (or onto another computer if that is where you’ll be running Prost!).
  • Rename the downloaded file (typically named mart_export.txt) to something more appropriate (e.g. YOUR_SPECIES_biomart_other_rnas.fa).
  • Build a BBMap database from the FASTA file (see Building BBMap Databases).
  • Update the Prost! configuration file (usually prost.config) to reflect the newly created BBMap database, for example:
[AnnotationAlignment3]
type: BiomartOtherRNAAnnotation
name: other
tool: bbmap
db: /path/to/YOUR_SPECIES_biomart_other_rnas
max_3p_mismatches: 0
max_non_3p_mismatches: 0
allow_indels: no