Shulou(Shulou.com)06/01 Report--

This article introduces how PAVIS, an online tool for gene annotation in the peak region, is very detailed. Interested friends can use it for reference. I hope it will be helpful to you.

PAVIS is an online tool that annotates the specific overlap of the peak region and genome.

For a gene, it is divided into the following areas, as shown below

The blue box represents the exon, the red line represents the intron, the transcriptional initiation site TSS at the 5 'end of the first exon and the transcriptional termination site TTS at the 3' end of the last exon. All sequences between TSS and TTS are spliced to form mature mRNA sequences. During the cutting process, the intron will be removed, leaving only the exon. In the process of translation of mRNA, there is an untranslated region at the 5 'end and 3' end, which is called UTR, corresponding to the green box in the diagram.

The upstream region of TSS is called promoter region, also known as upstream. Because there is no clear definition of length, in actual processing, we usually take a fixed threshold, such as 2kb, etc.; correspondingly, the region downstream of TTS is called downstram, which is also a fixed length.

The usage of the online tool is as follows: first select the corresponding gene annotation, define the length of upstream and downstream, and then upload the peak file in bed format, as shown below

On the results page, first show the proportion of each part in a table

In addition, pie charts and bar charts are used to show the proportion of each part, as shown below

This is the end of PAVIS, an online tool for gene annotation in the peak region. I hope the above content can be of some help and learn more. If you think the article is good, you can share it for more people to see.

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