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What this article shares to you is about how to understand the tandem repeat sequence search tool Tandem Repeats Finder. The editor thinks it is very practical, so I share it with you. I hope you can get something after reading this article.

Tandem Repeats Finder, or TRF for short, is a tool for finding tandem repeat sequences, which is integrated into the repeatmasker program.

Through the online service of the official website, you can quickly grasp the usage of the software and provide three options, as shown below. The difference between these three options lies in the number of adjustable parameters. Let's first run it with the default parameters.

Click the Basic link, jump to the following page, upload the corresponding sequence file in fasta format, or paste the corresponding sequence in the text box, and then click the Submit sequence button to submit.

In the jump link, click on the red box below to view the results of the analysis

1. Summary of the results of all sequences

On this page, you will list all the sequence ID that have detected repetitive sequence regions. Clicking on the name of each sequence will take you to the detailed page of the sequence.

two。 Summary of all repeating regions on a sequence

On this page, you will give a summary of all the repeated sequences in a sequence in the form of a table. Click Table Explanation to view the detailed explanation of the header; click the ID of the repeating region in the first column to jump to the detailed page.

3. Repeat sequence detail page

On this page, the sequence information of the repeating region is given, which is shown below. As you can see, it is a repetitive region with ACTC as motif.

In addition to online services, you can also download the software to run locally. The download link is as follows.

Https://tandem.bu.edu/trf/trf.download.html

For the linux server, it is recommended to rename the file after the download is completed to facilitate the call. The code is as follows

Chmod + x trf409.linux64ln-s trf409.linux64 trf

The usage of the software is as follows

Trf / home/xudl/soft/SSRIT/input.fasta 2 7 7 80 10 50 500-f-d-m

Here I have all adopted the default parameters. After running successfully, a lot of files will be generated in the current directory, in which the html file is consistent with the official website. Just check the html file directly.

This is how the tandem repeat search tool Tandem Repeats Finder is understood. The editor believes that there are some knowledge points that we may see or use in our daily work. I hope you can learn more from this article. For more details, please follow the industry information channel.

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