How to understand Rfam database
This article introduces you how to understand the Rfam database, the content is very detailed, interested friends can refer to, hope to be helpful to you.
Rfam is a database of RNA classification information, which classifies all kinds of RNA and cis-acting elements according to the results of multiple sequence alignment, the consistency of secondary structure and covariance model.
Http://rfam.xfam.org/
The latest version is 14.0. in the Rfam database, it includes the following three functional types of molecules
NcRNA genes
Cis-regulatory elements
Self-splicing RNAs
Further divide it into more detail, as shown in the following list
When classifying these data, two levels of classification are provided, family and clan. For family, its members are the various types of RNA; mentioned above; for clan, its members are individual family.
Through the Browser function of the official website, you can easily browse the contents of the database.
1. Clan
Each clan is uniquely identified by a number starting with CL, as shown below
The CL00051 in the figure above, for example, contains 11 family. The details are as follows
2. Family
Each family is uniquely identified by a number starting with RF, as shown below
The RF00005 in the figure above is an example. The family name is tRNA and the corresponding type is Gene; tRNA. The family contains RNA molecules from 9934 species, of which 536 have three-dimensional structural information.
For the information of multi-sequence alignment, both seed and full are provided, in which seed is the result of multi-sequence alignment of known members of the family by hand, and full is the result of multi-sequence alignment of all members of the family.
3. Genome
The hint is as follows
Taking human as an example, you can see the corresponding number of sequences and the number of family
4. Sequence
Each sequence is uniquely identified by a number that begins with CM, as shown below
The sequence details of CM000683.2 are as follows
Through the FTP function, you can download the contents of the database. The FTP link is as follows
Ftp://ftp.ebi.ac.uk/pub/databases/Rfam
The database provides not only the sequence information in fasta format, but also the CM model. Through infernal software, we can use these models to judge the RNA sequence and analyze the family information corresponding to the RNA sequence.
On how to understand the Rfam database to share here, I hope that the above content can be of some help to you, can learn more knowledge. If you think the article is good, you can share it for more people to see.
