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This article will explain in detail what is the use of GreeNC database for you. The editor thinks it is very practical, so I share it with you as a reference. I hope you can get something after reading this article.

The GreeNC database contains lncRNA information about plants and algae at the following URL

Http://greenc.sciencedesigners.com/wiki/Main_Page

The lncRNA in the database is the result of software prediction, and the pipeline is shown below.

After assembling the transcript using RNA_seq data, go through the following screening steps

Select transcripts whose length is greater than 200nt

Select transcripts whose ORF length is less than 360nt (protein less than 120 amino acids)

Compare with swiss-prot protein database, select transcripts without comparison or use CPC software to predict protein coding potential, select transcripts with predicted results as non-coding, and take the combination of the two methods as candidate lncRNA.

Compare with miRBase,Rfam database, select the transcript that is not matched as the final lncRNA

For the predicted lncRNA sequence, the repetitive elements are analyzed by Repeatmasker software. All predicted lncRNA are divided into the following two categories

High confidence

Low confidence

There is no comparison with swissport. CPC software predicts that it is non-coding, and there is no comparison between miRBase and Rfam databases. At the same time, lncRNA that meets these three conditions is classified as high confidence. If only two of these conditions are met, it is classified as low confidence;. If a lncRNA has too many repetitive elements, it is also classified as low confidence.

At present, the database contains the lncRNA information of 49 species. Taking rice Oryza sativa as an example, the search results are as follows.

By default, only 5 lncRNA messages are displayed. Through the more on the lower right, you can view the complete result, as shown below.

1. Genes

2. Transcripts

The strategy of predicting lncRNA in this database is relatively strict, which is worth using for reference.

This is the end of this article on "what is the use of GreeNC database". I hope the above content can be helpful to you, so that you can learn more knowledge. if you think the article is good, please share it out for more people to see.

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