Click the Blue Arrow to change slides
Clickable Table of Content
Return here by clicking the blue banner in the top right corner.
Besides this tutorial, snoDB internally links to the following:
- Version: Description of the updates applied as well as copies of previous files for each version.
- About: Textual explanation of the site's components with references and contact information.
- Statistics: Graphical representations of some of the data found in snoDB.
- Experiment Details: Page illustrating the RNA-Seq pipeline used to obtain the abundance data.
- rRNA Chemical Modifications: Whole interactive section on rRNA modified sites, containing snoRNA-rRNA interactions, graphical rRNA representation, conversion table between different rRNA versions, and finaly, graphs representing rRNA modication levels (2'-O-methylation or pseudouridylation), per position, on rRNAs.
- snoRupdate: Simple tool that completes a gtf file (Ensembl or RefSeq) with snoRNAs present in snoDB and missing in a provided annotation.
- Sequence Search Tool: Sequence similarity search (developped by RNACentral ) that enables the comparison of any query sequence against a comprehensive collection of ncRNAs.
- Detail pages: Clicking on snoDB ID links to individual pages for each entry.
snoDB Links to the Following Resources:
snoRNA Databases
snoRNABase snOPY snoRNA Atlas
General Resources
RNAcentral Ensembl RefSeq NCBI HGNC Rfam
The Human Protein Atlas
snoRNA-RNA interaction
RISE DATABASE Curated Articles
Main Search: Search 1 or More snoRNA Symbols
Global Search: Matches strings across entire table
(Including invisible columns: See Column Visibility for details)
Example -> Copy snora2a snord7[7-9](Regex for snord77 78 & 79) into the search bar and press Enter:
(Query results can be downloaded: See Download section for details)
Columns Search: Find exact matches within Column Groups
(Like Global Search, supports multiple space-separated terms and regex)
snoRNA Names ex: snord53 u13
Host Names ex: EIF4A2 UTP5
External IDs ex: HGNC:32711 NR_002741
Targets ex: 28S-3866 CHST7
(Query results can be downloaded: See Download section for details)
Regex Examples
| Regex | Search Box | Effect |
|---|---|---|
| snora2 snora2\D | snoRNA Names | Show snoRNAs with the same name and if they have varying end letters |
| nr_\d+ | External IDs | Show all entries with a Refseq ID |
| hgnc:\d+ | External IDs | Show all entries with an HGNC ID |
| hgnc:\d.*ensg\d.*nr_\d+ | External IDs | Show all entries with an HGNC ID, an Ensembl ID & a Refseq ID |
| ^(?!.*(hgnc|nr_)).*$ | External IDs | Show all entries without an HGNC or Refseq ID |
Toggle Column Visibility with buttons
Columns are grouped by similar data types and color coded to match columns in their group
Individual columns can be toggled by clicking on Column Visibility
Reorder Columns & Select Rows
Drag and drop Columns to re-order them.
Click on rows to highlight them.
- Hold Ctrl (Command on Mac) + Click = select non-contiguous rows
- Hold Shift + Click = select contiguous rows
