Introduction to PHI Database

Phi is a database of pathogenic bacteria, as of August 1, 2017, the latest version is 4.3, the database contains information on tested pathogenic bacteria, including 176 from animal pathogenic bacteria, 227 from plant pathogenic bacteria, 3 pathogenic bacteria from fungi;

The specific information for the database in version 4.3 is as follows:

A total of 4,775 genes, the interaction of 8,610, pathogenic bacteria have 264 species, 173 species of the host, the disease has 428 species, References reference 2330 kinds

The database URL is as follows:

http://www.phi-base.org/index.jsp

In the records for the database, there are several more commonly used fields that contain the following information:

Gene name: Names of genes

HOSE species: Name of the host species

Pathogen species: The name of the pathogen

Disease Name: disease names

Phi-base the number of the Accessionid:phi-base database

Phenotype Mutant: Phenotype changes caused by pathogenic bacteria

Experimental EVIDENCE: Experimental evidence

Multiple MUTATION:

Taking the gene ACPC as an example, the retrieval

Enter the name of the gene in the input box and click the Search button to retrieve the following results:

The input box on the left side of the picture provides different filter items that can be further filtered based on the year and other factors, and the table on the right is the final result retrieved.

Phi-base is free to download, the first need to register an account, click the Download button will prompt to register an account, the process of registration is not detailed, the registration is completed after you can see the download link:

Phi-base offers two ways to download:

The first kind: Download the sequence of the FASTA format, you can easily build a local version of the blast database, the function of the gene annotation

The second type: The entire database in CSV format, which is more comprehensive in the way of downloading information

The download to the Fasta section reads as follows:

>a0a023h5d8#phi:6442#eepr#615#serratia_marcescens#reduced_ Virulencemdnnhqkfdsqsianrvrelflhygigkrqharelsrildlsfshahrklkgqspwtleqinsvaaalgetpaaiadlsaehettepnmardaiffvagvampcvghigdel Pagrpaefvalrvegqwhiyradeapagprygv>a0a023na98#phi:3354#rtxa1#672#vibrio_vulnificus#reduced_ Virulencemgkpfwrsveyfftgnysaddgnnsivaigfggeihayggddhvtvgsigakvytgsgndtvvggsaylrvedttghlsvkgaagyadinksgdgnvsfagaaggvsidhlg Nhgdvnyggaaayngitrkglsgnvtfkgaggy

It can be seen as a protein sequence, which can be annotated by the BLASTP function of the gene's pathogenicity

The CSV format is as follows:

CSV file for all records of the entire database, contains a lot of fields, the more important or the previous several fields;

Reference: https://www.ncbi.nlm.nih.gov/pubmed/16381911

Introduction to PHI Database