What kind of database is PlncRNADB?

This article mainly shows you "what a database PlncRNADB is", which is easy to understand and clear. I hope it can help you solve your doubts. Let the editor lead you to study and learn this article "what a database PlncRNADB is."

LncRNA plays an important role in life activities, not only in mammals, but also in plants. At present, there are few studies on lncRNA in plants compared with animals, only rice, poplar, alfalfa, cotton and other species have been reported.

PlncRNADB is a database dedicated to the analysis of lncRNA in plants.

Http://bis.zju.edu.cn/PlncRNADB/index.php

The whole process of building the database is divided into three steps, as shown below

The corresponding RNA_seq sequencing reads of species was collected from GEO database, and the transcript sequence was obtained by strategy assembly of tophat+cufflinks.

First, remove transcripts whose length is less than 200nt, then filter out transcripts whose ORF length is larger than 120AA, and finally predict the protein coding potential of transcripts by CPAT software, so as to identify lncRNA transcripts.

After lncRNA is identified, the interaction between lncRNA and protein is predicted through catRAPID online service.

The database contains the lncRNA information of the following four species.

Arabidopsis lyrata

Arabidopsis thaliana

Populus trichocarpa

Zea mays

Take Arabidopsis thaliana as an example, you can view specific lncRNA information through Noncoding RNAs, as shown below

Click Entry to view detailed information, including chromosome location, sequence, expression profile and other data, as shown below

Through the lncRNA menu of the navigation bar, you can predict lncRNA, upload the sequence in fasta format, and then select the corresponding threshold, as shown below

From the Network menu in the navigation bar, you can view the interaction between lncRNA and protein, as shown below

Click Entry to view the visualization results, as shown below

From the SNP menu of the navigation bar, you can view the SNP site on the lncRNA, as shown below

This database provides an idea for the study of lncRNA in plants, and its method for predicting the interaction between lncRNA sequences and lncRNA-protein is worth using for reference.

The above is all the contents of the article "what is a database of PlncRNADB". Thank you for reading! I believe we all have a certain understanding, hope to share the content to help you, if you want to learn more knowledge, welcome to follow the industry information channel!