How to use IRESfinder to analyze the protein coding potential of cyclic RNA
This article shows you how to use IRESfinder to analyze the protein coding potential of circular RNA. The content is concise and easy to understand. It will definitely brighten your eyes. I hope you can get something through the detailed introduction of this article.
The 5 'cap structure of eukaryotic mRNA can mediate the binding of ribosomes, thus opening the translation process. CircRNA is classified as a kind of non-coding RNA because it is a closed ring structure and the 5' cap structure is missing.
With the further study of cyclic RNA, some scientists have found that some cyclic RNA can encode proteins. In addition to the common 5 'cap structure mediating ribosomal binding, there is a special case in which there is a 150-250bp sequence on some genes that can be folded into a tRNA-like structure, mediating ribosome binding to RNA and translating the initiation protein. Such sites are called internal ribosome entry site sequences, Internal ribosome entry site, or IRES for short.
The translation process is realized through IRES on the cyclic RNA that can encode proteins. As an example, the protein coding potential of cyclic RNA is studied. Some scholars have developed software to recognize IRES. IRESfinder is such a software to identify IRES sites in eukaryotes.
Using 583 human IRES sequences verified by experiments, 19 kmer sequences were selected to distinguish between IRES and non-IRES sequences. in this paper, the kmer distributions of two sequences in the test data set are given.
In the figure above, there are only 18 kmer, and another kmer is T. you can see that the frequency distribution of these kmer is different between IRES and non-IRES sequences.
The software is developed with Python, and the basic usage is as follows
Python IRESfinder.py-f circRNA.fa-o IRES.out.xls
The-f parameter specifies the input sequence in fasta format, and the-o parameter specifies the output result file. The contents of the output file are shown below
ID Index Scorehsa_circ_0018046 IRES 0.817344005hsa_circ_0039868 IRES 0.795083668hsa_circ_0089160 IRES 0.53322605hsa_circ_0048972 IRES 0.784080068hsa_circ_0018658 IRES 0.745230164hsa_circ_0067857 IRES 0.704497116hsa_circ_0019137 IRES 0.742607966hsa_circ_0063162 IRES 0.738372532hsa_circ_0087609 IRES 0.793042932hsa_circ_0006254 IRES 0.64587644
Through this software, we can quickly analyze and get the IRES sequence information on RNA, but the false positive result of the software must be very high, and the follow-up should be verified by experimental means.
The above is how to use IRESfinder to analyze the protein coding potential of circular RNA. Have you learned the knowledge or skills? If you want to learn more skills or enrich your knowledge reserve, you are welcome to follow the industry information channel.
