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How to understand the KEGG Orthology database, many novices are not very clear about this, in order to help you solve this problem, the following editor will explain for you in detail, people with this need can come to learn, I hope you can gain something.

We often use the KEGG database to study the function of genes, while in the KEGG database, the direct storage of molecular functions is the KEGG Orthology database.

KEGG Orthology is referred to as KO, and each record in the database is uniquely identified by K number. Based on the assumption that homologous genes have similar functions, the function of genes is expanded. For the genes whose functions are clearly studied in a species, we search for the homologous genes of the gene in different species, define these homologous genes as an orthology, and use the function of the gene as the function of the orthology; in this way, we will make use of the study of the gene function of different species and provide a comprehensive database to study the gene function.

Pathway,module and other databases are built on the basis of KO database, KO can be said to be in the core position of a database in KEGG, so it is particularly important to understand KO database.

For a specific KO, under this KO is a series of genes that can be derived from different species but have the same function. Take K00161 as an example, the list of corresponding homologous genes can be found on the official website of KEGG.

Open the link http://www.genome.jp/kegg/ko.html and type K number in the text box of the query, as shown in the following figure:

Click the Orthology table button, and you can see the specific gene list on the jump page, as shown in the following figure.

In the drop-down list, you can also screen for species, such as showing only the genes of Animals.

For known genes, the corresponding functions can be found directly in the database, so for newly discovered genes, how to use KO database to study their functions?

According to the definition of homologous genes, those with sequence similarity of more than 80% are defined as homologous genes. For genes with unknown functions, we only need to find homologous genes with known functions according to sequence alignment.

The KEGG official website provides an online tool, BlastKOALA. This tool is based on blast alignment, compares the input gene sequence with the sequence in the KEGG Gene database, finds the best matching gene, and assigns the corresponding K number to the queried gene.

1. First enter the sequence of the gene with the query in the text box

two。 Set the corresponding species information to reduce the range of species queried.

3. Select the gene set database for retrieval according to the actual situation

4. Finally, enter the email address and submit the task.

First, an email will be sent to your mailbox, and you must click on the link in this email to start your work. When it is over, another email will be sent to you, and you can see the final analysis results through the link in the email.

KO database is the basic database for the study of gene function, each KO corresponds to a series of genes with the same function, these genes can come from different species.

Based on the principle of sequence alignment, we can use KO database to study the function of new genes.

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