Krivonos, D. V. | Search bioRxiv

bioRxiv2022

FunFun: ITS-based functional annotator of fungal communities

Fungi are inseparable companions of human life, they can be found in both the environment and human organs including skin, respiratory tract and gut. Studies of fungal communities are of great interest to modern biology, partially due to their specific way of life and the presence of unique biochemical pathways they have. Fungi have been shown to be both producers of useful compounds, such as antibiotics and organic acids, and pathogens of various diseases. When considering the selected fungal community, in a number of cases it is rather difficult to evaluate its functional capabilities, which is partially caused by some technical difficulties in the analysis and annotation of whole eukaryotic genomes. In practice, the taxonomic composition of fungal communities is determined using short marker sequences. The most popular fungal taxonomy markers are ITS (internal transcribed spacer) sequences. Here, we present FunFun, the instrument that allows to evaluate the functional content of an individual fungus or mycobiome based on ITS sequencing data.

bioinformatics↗

bioRxiv2021

BioCAT: PSSM-based algorithm to search biosynthetic gene clusters producing nonribosomal peptides with known structure

MotivationNonribosomal peptides are a class of secondary metabolites synthesized by multimodular enzymes named nonribosomal peptide synthetases and mainly produced by bacteria and fungi. It has been shown that non-ribosomal peptides have a huge structural and functional diversity including antimicrobial activity, therefore, they are of increasing interest for modern biotechnology. Methods such as NMR and LC-MS/MS allow to determine a peptide structure precisely, but it is often not a trivial task to find natural producers of them. Today, the search is usually performed manually, mostly with tools such as antiSMASH or Prism. However, there are cases when potential producers should be found among hundreds of strains, for instance, when analyzing metagenomes data. Thus, the development of automated approaches is a high-priority task for further nonribosomal peptides research. ResultsWe developed BioCAT, a two-side approach to find biosynthetic gene clusters which may produce a given nonribosomal peptide when the structure of interesting nonribosomal peptide has already been found. Formally, BioCAT unites the antiSMASH software and the rBAN retrosynthesis tool but some improvements were added to both gene cluster and peptide chemical structure analyses. The main feature of the method is an implementation of position specific score matrix to store specificities of nonribosomal peptide synthetase modules, which has increased the alignment quality in comparison with more strict approaches developed earlier. An ensemble model was implemented to calculate the final alignment score. We tested the method on a manually curated nonribosomal peptides producers database and compared it with a competing tool called GARLIC. Finally, we showed the method applicability on several external examples. AvailabilityBioCAT is available on the GitHub repository or via pip Contactkonanovdmitriy@gmail.com

bioinformatics↗