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\begin{document}

\title{HMSS2: an advanced tool for the analysis of sulfur metabolism, including
organosulfur compound transformation, in genome and metagenome
assemblies}



\author[1]{Tomohisa Tanabe}%
\author[1]{Christiane Dahl}%
\affil[1]{Rheinische Friedrich-Wilhelms-Universität Bonn}%


\vspace{-1em}



  
  \date{May 27, 2024}


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\begin{abstract}
The global sulfur cycle has implications for human health, climate
change, biogeochemistry, and bioremediation. The organosulfur compounds
that participate in this cycle not only represent a vast reservoir of
sulfur, but are also used by prokaryotes as sources of energy and/or
carbon. Closely linked to the inorganic sulfur cycle, it involves the
interaction of prokaryotes, eukaryotes, and chemical processes. However,
ecological and evolutionary studies of the conversion of organic sulfur
compounds are hampered by the poor conservation of the relevant pathways
and their variation even within strains of the same species. In
addition, several proteins involved in the conversion of sulfonated
compounds are related to proteins involved in sulfur dissimilation or
turnover of other compounds. Therefore, the enzymes involved in the
metabolism of organic sulfur compounds are usually not correctly
annotated in public databases. To address this challenge, we have
developed HMSS2, a profiled Hidden Markov Model-based tool for rapid
annotation and synteny analysis of organic and inorganic sulfur cycle
proteins in prokaryotic genomes. Compared to its previous version
(HMS-S-S), HMSS2 includes several new features. HMM-based annotation is
now supported by non-homology criteria and covers the metabolic pathways
of important organosulfur compounds, including dimethylsulfpopropionate,
taurine, isethionate, and sulfoquinovose. In addition, the calculation
speed has been increased by a factor of four and the available output
formats have been extended to include iTol compatible datasets, and
customised sequence FASTA files%
\end{abstract}%



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