Browse RNA sequences in a species or taxonomic group of interest

To list all ncRNAs in a particular species, type the species name in the search bar and select the species in the Organism facet. Alternatively, you can use the syntax:

taxonomy:"NCBI_TAXID"

where NCBI_TAXID is the NCBI taxonomy identifier (taxid). For example, taxonomy:”10090″ will return all sequences from Mus musculus, which has the assigned NCBI taxid of 10090.

For the most accurate results, we recommend using the “Organism” facet or entering NCBI taxids because keyword-based queries can be ambiguous (for example, a search for Bacillus matches both Bacteria and Eukaryotes).

It is also possible to search for ncRNA sequences from any taxon using the following syntax:

tax_string:"viridiplantae" 

where tax_string is the taxonomic lineage for a species. Note the use of the Latin taxon name (“viridiplantae”, not “plants”).

Use advanced text search syntax

As shown above, it is possible to construct advanced queries using the Lucene query syntax, see EBI search documentation for more details. The following section provides examples for common use cases.

Use double quotes

To make sure that the results contain the exact query string, surround the query with double quotes. For example, if you are looking for a specific microRNA like hsa-mir-126, run the following search:

"hsa-mir-126"

A search without double quotes will also match hsa-mir-1261, hsa-mir-1262 and other sequences.

Use logic operators

The search supports logic operators, such as AND, OR and NOT. For example, one can identify microRNAs from miRBase that are not found in RefSeq or Ensembl (note the use of parentheses for grouping the search terms):

rna_type:"miRNA" AND expert_db:"miRBase" NOT (expert_db:"RefSeq" OR expert_db:"Ensembl")

Limit sequence length

One can restrict the length of the sequences, for example the following search returns rRNAs between 1400 and 1500 nucleotides long (it is also possible to use the sequence length slider shown in Figure 3).

rna_type:"rRNA" length:[1400 TO 1500]

For a full list of searchable fields check the EBI Search documentation.