CANT-HYD: a curated database of phylogeny-derived hidden markov models for annotation of marker genes involved in hydrocarbon degradation

The Calgary approach to ANnoTating HYDrocarbon degrading enzymes is a database used for robust and accurate annotation of genes associated with aerobic and anaerobic hydrocarbon degradation.

Implementation

1. Download individual or concatenated HMM files from this GitHub repository

2. Annotate protein-coding gene predictions from microbial whole genomes and metagenome-assembled genomes using CANT-HYD HMMs implemented in HMMER

hmmsearch --tblout hmmsearch_metagenome.tblout CANT-HYD.hmm metagenome_proteins.faa > hmmsearch_metagenome.out

         Options:

         a. --cut_tc for trusted cutoff

         b. --cut_nc for noise cutoff

         c. no option, for exploring genes below the noise cutoff

Article

Khot V, Zorz J, Gittins DA, Chakraborty A, Bell E, Bautista MA, Paquette AJ, Hawley AK, Novotnik B, Hubert CRJ, Strous M and Bhatnagar S (2022) CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation. Front. Microbiol. 12:764058. doi: 10.3389/fmicb.2021.764058