MetaHMM: A Webserver for Identifying Novel Genes with Specified Functions in Metagenomic Samples

TL;DR

MetaHMM is a user-friendly webserver that enables researchers to identify novel genes with specific functions in metagenomic datasets using homology-based modeling and sequence search techniques.

Contribution

It introduces an accessible web platform that automates model building and gene homology searches in metagenomic samples, enhancing gene discovery efforts.

Findings

Automates gene homology detection in metagenomes.

Utilizes established bioinformatics tools for model building and searching.

Provides a publicly available resource for microbial gene discovery.

Abstract

The fast and affordable sequencing of large clinical and environmental metagenomic datasets opens up new horizons in medical and biotechnological applications. It is believed that today we have described only about 1\% of the microorganisms on the Earth, therefore, metagenomic analysis mostly deals with unknown species in the samples. Microbial communities in extreme environments may contain genes with high biotechnological potential, and clinical metagenomes, related to diseases, may uncover still unknown pathogens and pathological mechanisms in known diseases. While the species-level identification and description of the taxa in the samples does not seem to be possible today, we can search for novel genes with known functions in these samples, using numerous techniques, including artificial intelligence tools, like the hidden Markov models (HMMs). Here we describe a simple-to-use webserver, the MetaHMM, which is capable of homology-based automatic model-building for the genes to be searched for, and it also finds the closest matches in the metagenome. The webserver uses already highly successful building blocks: it performs multiple alignment by applying Clustal Omega, builds a hidden Markov model with HMMER components of hmmbuild and uses hmmsearch for finding similar sequences to the specified model in the metagenomes. The webserver is publicly available at \url{https://metahmm.pitgroup.org}.