MINRbase : a framework for the interactive exploration of mitochondrial and nuclear rRNA fragments

MINRbase v1.0 : a database for the interactive exploration of mitochondrial and nuclear rRNA fragments

07/01/2023 stats: 130,238 expressed rRFs | 11,632 datasets | 130,420 genomic instances

MINRbase glossary

Term Definition
rRF We report rRNA fragments (rRFs) with lengths 16-50 nt.
rRNA fragment see rRF definition.
type of rRF
  • 5'-rRFs: these are rRFs whose 5'-end matches the 5'-end of the parental rRNA.
  • 3'-rRFs: these are rRFs whose 3'-end matches the 3'-end of the parental rRNA.
  • i-rRFs ("internal" rRFs): these rRFs lie wholly inside the parental rRNA and are neither 5'-rRFs nor 3'-rRFs.
  • 5'-s-rRFs: these are rRFs whose 5'-end matches the 5'-end of a 45S spacer.
  • 5'-s-rRFs: these are rRFs whose 5'-end matches the 5'-end of a 45S spacer.
  • 3'-s-rRFs: these are rRFs whose 3'-end matches the 3'-end of a 45S spacer.
  • i-s-rRFs: these rRFs lie wholly inside a spacer and are neither 5'-s-rRFs nor 3'-s-rRFs.
  • x-rRFs ("crossing" rRFs): these are rRFs that straddle an rRNA and a spacer, or an rRNA and an adjacent genomic region other than a spacer.
For more information on i-tRFs visit here.
RPM Reads per million (RPM) is a measure of abundance of a rRF among the primary raw reads of a dataset. To calculate the RPM two values are required, a) the total number of sequenced reads and b) the number of times the rRF was encountered after mapping.
Dataset number (with RPM ≥ x) The total number of datasets that were submitted in MINRbase and reported the rRF with an RPM value of more than or equal to x. If no RPM requirement is stated then x equals 1. MINRbase automatically discards rRFs with an RPM value of RPM < 1.
Expressed rRF MINRbase generates all possible potential rRFs and does not wait for them to be reported. Some of those rRFs have not yet (or may never be) found in any dataset.
A rRF is characterized as expressed if it is included in at least one dataset that has been submitted in MINRbase with RPM ≥ 1 (see also dataset number). Otherwise it is considered not-expressed.
A user can select to view all possible rRFs or expressed rRFs only.
Unique ID (sequence derived) License plates or rRF license plates or Sequence derived MINRbase unique IDs, are a rRNA fragment ID that depends solely on the rRF's sequence which transcends assemblies and species. Find out more or generate convert your own by using MINTplates.
License Plate See "Unique ID (sequence derived)" definition.
rRNA name See this list of rRNAs accepted.
Candidate mature rRNA sources Candidate mature rRNA sources or Parental rRNAs are the rRNAs from which the rRF can be derived. Those are the rRNAs whose mature sequence (or their post-modifications) contains the rRFs.
Parental rRNAs See "Candidate mature tRNA sources" definition.