AUTHOR=Khot Varada , Zorz Jackie , Gittins Daniel A. , Chakraborty Anirban , Bell Emma , Bautista María A. , Paquette Alexandre J. , Hawley Alyse K. , Novotnik Breda , Hubert Casey R. J. , Strous Marc , Bhatnagar Srijak 

TITLE=CANT-HYD: A Curated Database of Phylogeny-Derived Hidden Markov Models for Annotation of Marker Genes Involved in Hydrocarbon Degradation

JOURNAL=Frontiers in Microbiology

VOLUME=12

YEAR=2022

URL=https://www.frontiersin.org/journals/microbiology/articles/10.3389/fmicb.2021.764058

DOI=10.3389/fmicb.2021.764058

ISSN=1664-302X

ABSTRACT=<p>Many pathways for hydrocarbon degradation have been discovered, yet there are no dedicated tools to identify and predict the hydrocarbon degradation potential of microbial genomes and metagenomes. Here we present the Calgary approach to ANnoTating HYDrocarbon degradation genes (CANT-HYD), a database of 37 HMMs of marker genes involved in anaerobic and aerobic degradation pathways of aliphatic and aromatic hydrocarbons. Using this database, we identify understudied or overlooked hydrocarbon degradation potential in many phyla. We also demonstrate its application in analyzing high-throughput sequence data by predicting hydrocarbon utilization in large metagenomic datasets from diverse environments. CANT-HYD is available at <ext-link ext-link-type="uri" xlink:href="https://github.com/dgittins/CANT-HYD-HydrocarbonBiodegradation" xmlns:xlink="http://www.w3.org/1999/xlink">https://github.com/dgittins/CANT-HYD-HydrocarbonBiodegradation</ext-link>.</p>