Tutorial on how the website works

Each tab corresponds to a page and explains what its components functionally do.

Bona fide set of sRNA with experimental validation

This set of sRNAs forms the core of our database. It consists of sRNA that have been hand-curated based on experimental evidence. If an sRNA could not be found in an article to have experimental support, then it was not included. This way, whichever sRNAs we have included has a high probability of being functionally active in bacterial transcriptome.

The columns are searchable based on the type of data inside. For example, to search for sRNAs that have been functionally validated in antibiotic sensitivity, one can search for "antibiotic" in the search bar corresponding to "Functional Analysis". The explanation for the other columns are given below:

  1. smallBARNA_ID: Unique ID generated for each sRNA...
  2. Literature Synonyms: Other synonyms that the sRNA is known as...
  3. Validated in PMIDs: Pubmed IDs of the articles...
  4. Validated in Species: Species in which the sRNA was originally validated...
  5. Validated in Genomes: Genbank Accession...
  6. Northern Blot: Whether or not the sRNA was validated...
  7. RT-PCR: Whether or not the sRNA was validated...
  8. qPCR: Whether or not the sRNA was validated...
  9. Functional Analysis: Whether or not the function of the sRNA was tested...
  10. Other Validations: Miscellaneous experimental methods...
  11. Differentially Expressed Under Conditions: Whether there is evidence of the sRNA being conditionally expressed...
  12. Validated in Tissues: The type of tissue in which the sRNA validation experiments were carried out...
Pan genome analysis using NCBI genomes and plasmids

Conservation across and within species is a strong signal of functionality. Other times the presence of sRNA in mobile elements in the genome or on plasmids also hints at functionality. To make this distribution easily accessible, we obtained complete chromosomes and plasmids available in NCBI and aligned our bona fide set across them.

Using the filtering options, users can identify sRNAs present in specific taxonomic groups. Each row represents the mapping of an sRNA to a chromosome or plasmid.

  1. smallBARNA ID: The sRNA ID from the bona fide set.
  2. No. of Chromosomes with Hits: Number of chromosomes mapped.
  3. No. of Genuses with Hits: Number of unique genuses mapped.
  4. No. of Plasmids with Hits: Number of plasmids mapped.
  5. No. of Species with Hits: Number of species mapped.
  6. No. of Strains with Hits: Number of bacterial strains mapped.
  7. Aligned against Genbank Acc: Genbank Accession of the match.
  8. Mapping Start Position: Start position of the match.
  9. Alignment Direction: Strand of the match.
  10. Aligned against species: Species name.
  11. Aligned against taxid: NCBI taxid.
  12. Aligned against strain: Strain name.
  13. Aligned against genome assembly: NCBI genome assembly.
  14. Aligned against: Plasmid or Chromosome: Location type.
sRNA profile page for individual sRNA

Each sRNA has a profile page with all its relevant information:

  • Evidence Information: Literature curated evidence.
  • Genus Species Information: Stacked barplots showing distributions.
  • Alignment Information: Subset of pan genome mapping.
  • Expression Information: Normalized expression values.
  • Articles: PMIDs and titles of references.
  • Genome CGView: Visualization of mappings.