<p>The info is actually in the <code>gene_biotype</code> column of my <code>wormGenes</code> data frame. I could select the rRNA genes using <code>dplyr::filter(wormGenes, gene_biotype == 'rRNA')</code>. Unfortunately, no description is available for the genes, so I will have to get it using the gene IDs.</p>

CC BY-SA 4.0
2018-06-20T21:39:24.590Z
2018-06-20T21:39:24.590Z
Biomagician
<p>Where can I find the DNA sequence of the <em>C. elegans</em> rRNA cluster?</p>

<p>Ideally, I would be able to do it using the command-line.</p>

<p>I've tried using <a href="https://www.ncbi.nlm.nih.gov/nuccore/?term=ribosomal%20RNA%20caenorhabditis%20elegans" rel="nofollow noreferrer">NCBI</a> but the results are unsatisfactory. I am interested in the DNA sequence that is in the current reference genome of <a href="http://wormbase.org/" rel="nofollow noreferrer">WormBase</a>.</p>

<p>I have tried using the Bioconductor biomaRt package and create a table containing the description but when I grep 'rRNA', I only get proteins doing things with rRNA. I used the following code:</p>

<pre><code>ensembl &lt;- biomaRt::useMart('ensembl', dataset = 'celegans_gene_ensembl')
wormGenes &lt;- biomaRt::getBM(attributes = c('external_gene_name', 'chromosome_name', 'start_position', 'end_position', 'gene_biotype', 'description'), mart = ensembl)
wormGenes[grep('rRNA', wormGenes$description), 6]

[1] "rRNA 2'-O-methyltransferase fibrillarin  [Source:UniProtKB/Swiss-Prot;Acc:Q22053]"      
[2] "Pre-rRNA-processing protein pro-1  [Source:UniProtKB/Swiss-Prot;Acc:Q22006]"            
[3] "Pre-rRNA-processing protein TSR1 homolog  [Source:UniProtKB/Swiss-Prot;Acc:Q19329]"     
[4] "rRNA methyltransferase 2, mitochondrial  [Source:UniProtKB/Swiss-Prot;Acc:O62251]"      
[5] "Probable rRNA-processing protein EBP2 homolog  [Source:UniProtKB/Swiss-Prot;Acc:Q09958]"
[6] "Putative rRNA methyltransferase  [Source:UniProtKB/TrEMBL;Acc:Q5CCJ2]" 
</code></pre>

<database><biomart><data-download><sequence-annotation>
Where can I find the DNA sequence of the C. elegans rRNA cluster?
# Where can I find the DNA sequence of the C. elegans rRNA cluster?

(Asked by: username_0 on 2018-06-20)

Where can I find the DNA sequence of the C. elegans rRNA cluster?
Ideally, I would be able to do it using the command-line.
I've tried using NCBI but the results are unsatisfactory. I am interested in the DNA sequence that is in the current reference genome of WormBase.
I have tried using the Bioconductor biomaRt package and create a table containing the description but when I grep 'rRNA', I only get proteins doing things with rRNA. I used the following code:
ensembl <- biomaRt::useMart('ensembl', dataset = 'celegans_gene_ensembl')
wormGenes <- biomaRt::getBM(attributes = c('external_gene_name', 'chromosome_name', 'start_position', 'end_position', 'gene_biotype', 'description'), mart = ensembl)
wormGenes[grep('rRNA', wormGenes$description), 6]

[1] "rRNA 2'-O-methyltransferase fibrillarin  [Source:UniProtKB/Swiss-Prot;Acc:Q22053]"      
[2] "Pre-rRNA-processing protein pro-1  [Source:UniProtKB/Swiss-Prot;Acc:Q22006]"            
[3] "Pre-rRNA-processing protein TSR1 homolog  [Source:UniProtKB/Swiss-Prot;Acc:Q19329]"     
[4] "rRNA methyltransferase 2, mitochondrial  [Source:UniProtKB/Swiss-Prot;Acc:O62251]"      
[5] "Probable rRNA-processing protein EBP2 homolog  [Source:UniProtKB/Swiss-Prot;Acc:Q09958]"
[6] "Putative rRNA methyltransferase  [Source:UniProtKB/TrEMBL;Acc:Q5CCJ2]"

**Tags:** database, biomart, data-download, sequence-annotation

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## 1 answers

### Answer by username_0 on 2018-06-20. Score: 1 | Accepted answer

The info is actually in the `gene_biotype` column of my `wormGenes` data frame. I could select the rRNA genes using `dplyr::filter(wormGenes, gene_biotype == 'rRNA')`. Unfortunately, no description is available for the genes, so I will have to get it using the gene IDs.


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