Research graph
References from MacSyFinder v2: Improved modelling and search engine to identify molecular systems in genomes. Local targets link to admitted publications; unresolved targets remain external evidence.
Supplementary Information for the MacSyFinder v2 article. figshare. Journal contribution
10.6084/m9.figshare.21936992 · 2023 · External reference
Test dataset for MacSyFinder (v2) and expected output files. figshare. Dataset
10.6084/m9.figshare.21581280.v1 · 2022 · External reference
A comprehensive test dataset for MacSyFinder v2 with TXSScan. figshare. Dataset
10.6084/m9.figshare.21716426.v1 · 2022 · External reference
Identification of protein secretion systems in bacterial genomes using MacSyFinder version 2
10.1101/2023.01.06.522999 · External reference
Identification of protein secretion systems in bacterial genomes
10.1038/srep23080 · 2016 · External reference
MacSyFinder: A Program to Mine Genomes for Molecular Systems with an Application to CRISPR-Cas Systems
10.1371/journal.pone.0110726 · 2014 · External reference
The Non-Flagellar Type III Secretion System Evolved from the Bacterial Flagellum and Diversified into Host-Cell Adapted Systems
10.1371/journal.pgen.1002983 · 2012 · External reference
An archaeal origin of the Wood–Ljungdahl H4MPT branch and the emergence of bacterial methylotrophy
10.1038/s41564-019-0534-2 · 2019 · External reference
Atypical organizations and epistatic interactions of CRISPRs and cas clusters in genomes and their mobile genetic elements
10.1093/nar/gkz1091 · 2019 · External reference
antiSMASH 6.0: improving cluster detection and comparison capabilities
10.1093/nar/gkab335 · 2021 · External reference
10.1007/b106453
10.1007/b106453 · 2005 · External reference
A catalogue of 1,167 genomes from the human gut archaeome
10.1038/s41564-021-01020-9 · 2021 · External reference
Evolution of Plasmid Mobility: Origin and Fate of Conjugative and Nonconjugative Plasmids
10.1093/molbev/msac115 · 2022 · External reference
CRISPRCasFinder, an update of CRISRFinder, includes a portable version, enhanced performance and integrates search for Cas proteins
10.1093/nar/gky425 · 2018 · External reference
Identifying Conjugative Plasmids and Integrative Conjugative Elements with CONJscan
10.1007/978-1-4939-9877-7_19 · 2019 · External reference
Integrative and conjugative elements and their hosts: composition, distribution and organization
10.1093/nar/gkx607 · 2017 · External reference
Conservation of gene order: a fingerprint of proteins that physically interact
10.1016/s0968-0004(98)01274-2 · 1998 · External reference
Conjugative DNA metabolism in Gram-negative bacteria
10.1111/j.1574-6976.2009.00195.x · 2010 · External reference
Diversification of the type IV filament superfamily into machines for adhesion, protein secretion, DNA uptake, and motility
10.1371/journal.pbio.3000390 · 2019 · External reference
The Evolution of Protein Secretion Systems by Co-option and Tinkering of Cellular Machineries
10.1016/j.tim.2020.01.005 · 2020 · External reference
Accelerated Profile HMM Searches
10.1371/journal.pcbi.1002195 · 2011 · External reference
Evolution of Conjugation and Type IV Secretion Systems
10.1093/molbev/mss221 · 2012 · External reference
The TIGRFAMs database of protein families
10.1093/nar/gkg128 · 2003 · External reference
Exploring Network Structure, Dynamics, and Function using NetworkX
2008 · External reference
The arms race between bacteria and their phage foes
10.1038/s41586-019-1894-8 · 2020 · External reference
Predicting Protein Function by Genomic Context: Quantitative Evaluation and Qualitative Inferences
10.1101/gr.10.8.1204 · 2000 · External reference
KEGG Mapper for inferring cellular functions from protein sequences
10.1002/pro.3711 · 2019 · External reference
Pathway Tools version 23.0 update: software for pathway/genome informatics and systems biology
10.1093/bib/bbz104 · 2019 · External reference
Evolutionary classification of CRISPR–Cas systems: a burst of class 2 and derived variants
10.1038/s41579-019-0299-x · 2019 · External reference
gem-pasteur/macsyfinder: MacSyFinder v2.1 (2.1)
10.5281/zenodo.7704885 · 2023 · External reference
Type IV pili: e pluribus unum?
10.1111/j.1365-2958.2008.06197.x · 2008 · External reference
SepF is the FtsZ anchor in archaea, with features of an ancestral cell division system
10.1038/s41467-021-23099-8 · 2021 · External reference
PanACoTA: a modular tool for massive microbial comparative genomics
2021 · External reference
Abundance and co-occurrence of extracellular capsules increase environmental breadth: Implications for the emergence of pathogens
10.1371/journal.ppat.1006525 · 2017 · External reference
Host control and the evolution of cooperation in host microbiomes
10.1038/s41467-022-30971-8 · 2022 · External reference
Pfam: A comprehensive database of protein domain families based on seed alignments
10.1002/(sici)1097-0134(199707)28:3<405::aid-prot10>3.0.co;2-l · 1997 · External reference
Genome-wide analysis of the Firmicutes illuminates the diderm/monoderm transition
10.1038/s41559-020-01299-7 · 2020 · External reference
Conservation of gene co-regulation in prokaryotes and eukaryotes
10.1016/s0167-7799(02)02032-2 · 2002 · External reference
Systematic and quantitative view of the antiviral arsenal of prokaryotes
10.1038/s41467-022-30269-9 · 2022 · External reference
MicroScope: an integrated platform for the annotation and exploration of microbial gene functions through genomic, pangenomic and metabolic comparative analysis
10.1093/nar/gkz926 · 2019 · External reference