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This article analyzes "how to understand the circular RNA database circBase". The content is detailed and easy to understand, "how to understand the circular RNA database circBase" interested friends can follow the editor's ideas slowly in-depth to read, I hope that after reading can be helpful to everyone. Let's follow the editor to learn more about "how to understand the circular RNA database circBase".

CircBase is a circular RNA database, which contains the circular RNA information of many species such as humans, mice and so on. Find_circ software is used to predict the circular RNA in the ribosomal library. The website of the database is as follows.

Http://www.circbase.org/

In this database, the ID of the circular RNA begins with the three-letter abbreviation of the species, such as hsa_circ_0018046, and records the position, source gene, sequence and other information of the head and tail of the circRNA on the chromosome. You can retrieve the database in the following three ways

1. Direct retrieval

In the search box of the home page, you can search according to the ID of the circular RNA, the name of the source gene, the name of the transcript, and so on.

The search results are as follows

The software identifies the circular RNA by detecting the reads on both sides of the junction. For a circular RNA, it can only give the position of the head and tail on the chromosome and the positive and negative chain information. The genomic length in the search result corresponds to the length between the head and tail of the circular RNA in the genome.

At the same time, the annotations of repetitive elements and genomic characteristics on the chromosome region corresponding to the circular RNA are also provided.

For the sequence information of circular RNA, compare it with the known transcripts according to the position of the head and tail chromosomes, select a best transcript, that is, best transciprt as a reference, and then determine the sequence of circular RNA after cutting, so as to get spliced length. It should be noted that the sequence obtained in this way is only the result of a letter prediction, which needs to be verified by experimental means.

The search results support the export of xlsx, txt, csv and other formats, as well as the sequence of annular RNA, as shown below

Support the export of genome sequences and cut sequences, but also can be extended upstream and downstream.

two。 List retrieval

Through the list search of the navigation bar, you can retrieve multiple records in turn, as shown below

Select the corresponding species, and then enter multiple ID to be retrieved.

3. Table browser

Similar to UCSC's table browser, it provides a more flexible filtering strategy. The search box is shown below.

Through the blat button, you can enter a query sequence in fasta format, and then compare it with the circRNA sequence in the database, as shown below

The query results are as follows

The database is free to download, you can download the list of annular RNA corresponding to species, and you can also download the corresponding sequence. At the same time, it also provides the source code of find_circ software, which can be used to analyze circRNA in your own sequencing data.

About how to understand the circular RNA database circBase to share here, I hope that the above content can make you improve. If you want to learn more knowledge, please pay more attention to the editor's updates. Thank you for following the website!

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