About piRBase and Tutorial
piRBase is a manually curated resource of piRNAs, which focused on piRNA function analyses as well as piRNA annotation.
piRBase introduction
piRNAs are a class of small RNAs that is most abundantly expressed in the animal germ
line. Numerous studies have shown that piRNAs have many important biological functions. A piRNA database for collection, annotation and structuring of these data will be a valuable contribution to the field, and we have therefore developed the piRBase platform for collection, annotation and structuring of various piRNA-related data.
1. piRBase release v1.0 released in 2014.
2. piRBase release v2.0 released in 2018.
3. piRBase release v3.0 released in 2021.
piRBase User manual
1 Overview
On the index page, we offer:
· search function
· information about piRBase
Click “READ MORE” to see more details.
· entry to functional modules of the website
· data statistics of piRBase
Click “READ MORE” to see more details.
· some tools for piRNA analysis.
Click “GET STARTED” to use the corresponding tool.
Also, user can enter into above functional modules by clicking bottons at top of the page.
2 Search piRNAs by piRBase id
Specify a search range (search in all piRNAs in piRBase or only in gold standard piRNA set), enter a piRNA id or a comma splitted list of multiple piRNA ids, then click “Search” botton to get results.
This page offers summary of piRNA items found in specified search range.
Click piRNA id to see the datail information.
Click the number to see a more detailed description of search result in table format. For example, click “38” to see datasets information.
3 Browse piRNAs, datasets, and piRNA clusters by species
Specify an organism, then click “Select” to browse all piRNAs of this organism.
You can change the number of items per page by clicking “Display” botton after filling in the text box next to it and jump to certain page by clicking “Page” botton after entering the page number. Besides, user can click “Download” to download data in .gz format.
Also, user can browse datasets or piRNA clusters with similar operations.
4 Search piRNAs by functional information
For instance, user can search repeat derived piRNAs by entering organism and types of repeats.
Similarly, other functional information about piRNAs such as target mRNA, lncRNA, and variants can be found in corresponding module.
5 View epigenetic information and piRNAs for a specified genomic region
Specify an organism and enter a genomic region like “1:64579378-64651122”, then click “Search” to view the epigenetic information (DNA methylation or H3K9me3 marker) and piRNAs in this region.
6 Download data
On the download page, user can download piRNA data in .fasta or .bed format. For example, user can click “aca.fa.gz” to download piRNA fasta file for Sea hare(aca).
