microbma / asgenedb

A manually curated arsenic functional gene database (AsgeneDB) was developed for rapid and accurate metagenomic analysis.

AsgeneDB: A functional gene database for metagenomic profiling of arsenic metabolism

A manually curated arsenic functional gene database (AsgeneDB) was developed for rapid and accurate metagenomic analysis.

Xinwei Song, Yongguan Zhu, Yongming Luo, Bin Ma*, Jianming Xu

Arsenic (As) is a kind of toxic metal-like element widely distributed in the world. To understand the microbial community of arsenic metabolism in the environment, we developed a curated arsenic functional gene database (AsgeneDB) covering four arsenic metabolic pathways (oxidative, respiratory, reduction and methylation processes), 59 arsenic biotransformation functional gene families and 414773 representative sequences. Here, protein sequences for As gene families were recruited from multiple public databases such as UniProt, KEGG, COG, eggNOG, arCOG and KOG. AsgeneDB covers 46 phyla and 1653 genera of bacterial archaea and fungi. It can quickly analyze the arsenic metabolism and transformation function of microbial communities by integrating multiple lineal homology databases with high specificity, comprehensiveness, representativeness and accuracy.

1. target_asgene.fasta: Fasta format representative sequences obtained by clustering curated sequences at 100% sequence identity. This file can be used for "BLAST" searching arsenic genes in shotgun metagenomes.

2. asgene.map: A mapping file that maps sequence IDs to gene names, only sequences belonging to arsenic gene families are included. This file is used to generate arsenic gene profiles from BLAST-like results against the database.

3. id_gene_tax_pathway.csv: Species information table of sequences.

4. length.txt: The file contains the length of amino acid sequences in AsgeneDB for standardizing arsenic gene abundance statistics.

5. gene_abundance.R : Script used to calculate and standardize gene abundance in samples.

6. sample_gene_tax.R : Script used to statistical information of functional species in samples.