What is the use of CANTATAdb database
This article mainly introduces the use of the CANTATAdb database, has a certain reference value, interested friends can refer to, I hope you can learn a lot after reading this article, the following let the editor take you to understand it.
The CANTATAdb database contains the lncRNA information in plants, and mainly identifies the lncRNA in plants by the way predicted by l software. At present, it contains 239631 lncRNA from 39 species. It is the largest plant lncRNA database at the following website.
Http://yeti.amu.edu.pl/CANTATA/
The RNA_seq data of plants were collected from the SRA of NCBI and the ENA database of EBI, and the transcript sequences were obtained by comparison and assembly, and then the lncRNA was predicted by CNCI software.
Through the Search menu of the navigation bar, you can select the species of interest from the drop-down list and view the corresponding lncRNA information. Take rice Oryza sativa as an example, the search box is as follows
CNCI software can be used to predict the results, peptide length, expression, exon number and other parameters to screen the results. The second part of the page shows the total number of screened results, as shown below
The third part is the final result, which is shown below.
In this database, each transcript ID begins with CNCT, and gives the chromosome position, the score value of CNCI software, the comparison result with swiss-prot protein database, the maximum peptide length, the maximum expression quantity, the number of exons and other information. Click Details to view the following details
1. Blast
two。 Expression quantity
3. Peptide prediction result
4. Sequence
The lncRNA information in the database can be downloaded free of charge, and two formats, FASTA and GTF, are provided, as shown below
The database contains the largest number of species, and plant lncRNA researchers can pay attention to this database.
Thank you for reading this article carefully. I hope the article "what's the use of CANTATAdb database" shared by the editor will be helpful to you? at the same time, I also hope you will support us and pay attention to the industry information channel. More related knowledge is waiting for you to learn!
