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This article will explain in detail what is the use of eggNOG database for you. The editor thinks it is very practical, so I share it with you as a reference. I hope you can get something after reading this article.

The prediction of lineal homologous proteins plays an important role in many fields, such as phylogeny, comparative genomics and so on. COG database has created a precedent of homologous protein database, followed by the emergence of new databases, and eggNOG is one of the most widely used databases.

The official website is as follows

Http://eggnogdb.embl.de/#/app/home

The full name of eggNOG is evolutionary genealogy of genes:Non-supervised Orthologous, which is extended and extended on the basis of COG algorithm. The unsupervised clustering algorithm based on graph structure is used to construct homologous protein clusters of eukaryotic, prokaryotic, virus and other species.

The latest version of the database is eggNOG 4.5.1, covering 2031 species of eukaryotes and prokaryotes, 352 kinds of viruses, and constructing 190000 homologous protein clusters.

Similar to COG, eggNOG classifies the functions of orthology group. Each category is represented by a letter. You can see the specific classification information in the following link.

Http://eggnogdb.embl.de/download/eggnog_4.5/COG_functional_categories.txt

26 classifications are available in the COG database and 25 in eggNOG, missing the following categories

X Mobilome: prophages, transposons

The other categories are exactly the same as the COG database. The OG number can be searched in the search box of the official website.

The retrieval results of COG5157 are as follows

In the search results, the protein sequence and species information contained under the orthology group can be viewed, and the corresponding sequence can also be downloaded. In addition, it also provides GO, KEGG, pfam, SMRT and other related function annotation information.

In addition to online retrieval, officials also provide API services to facilitate programs to crawl corresponding data. Examples are as follows

Http://eggnogapi.embl.de/nog_data/text/fasta/ENOG410ZSWV

All the protein sequences under the orthology group of ENOG410ZSWV can be obtained through the above API link. For more usage, please refer to the official documentation.

The official website also provides the following two annotation services

1. Search

Query only one sequence at a time. Enter the protein sequence in fasta format and select the corresponding species.

2. EggNOG-mapper

Support multiple sequences of NOG comments, provide online services, you can also download software to run locally.

Support diamond and hmmer two kinds of alignment software, when the sequence number is less than 1000, select hmmer, when the sequence is more than 1000, select diamond, the speed is faster. For the installation and use of the local version of eggNOG-mapper, please refer to the following documentation

Https://github.com/jhcepas/eggnog-mapper/wiki

The official website provides a download service, which can download the complete database or select the appropriate sub-database according to the species, as shown below

Through the eggNOG database, we can annotate the homologous proteins of the new protein sequences and explore their functions.

This is the end of this article on "what is the use of eggNOG database". I hope the above content can be helpful to you, so that you can learn more knowledge. if you think the article is good, please share it out for more people to see.

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