TABLE 2.
Bioinformatics tools for ARG annotation from whole genome and metagenome datasets.
| S. No | Bioinformatic tool | Web address | Description | Updated date | References |
| 1 | ResFinder | https://cge.cbs.dtu.dk//services/ResFinder | Identifies acquired and chromosomal mutation from shotgun reads | 02-06-2020 | Zankari et al., 2012 |
| 2 | ARGs_OAP | https://smile.hku.hk/SARGs | Identifies ARGs in metagenomic data thought galaxy server | 2020.07.15 | Yin et al., 2018 |
| 3 | ARDB | http://ardb.cbcb.umd.edu/ | A database of ARGs. However, the ARDB is no longer maintained | July 3, 2009. | Liu and Pop, 2009 |
| 4. | The Comprehensive Antibiotic Resistance Database (CARD) | https://card.mcmaster.ca/ | A database of ARGs that are peer reviewed. It includes software to predict resistome from protein, genome, or metagenomics datasets | Monthly updated | Alcock et al., 2020 |
| 5 | ARGO - antibiotic resistance genes online | http://bioinformatics.org/argo/beta/submissions/submit_sequence.php | A database of ARGs with majority of sequence from β - lactamase | NA | Scaria et al., 2005 |
| 6. | DeepARG | http://bench.cs.vt.edu/deeparg | It provides web service and command line tools for prediction of ARGs from metagenome data using machine learning approach | NA | Arango-Argoty et al., 2018 |
| 7. | Graphing Resistance Out Of meTagenomes (GROOT) | https://github.com/will-rowe/groot | It provides a resistome profile from metagenomic datasets | May 11 2020 | Rowe and Winn, 2018 |
| 8. | KmerResistance | https://cge.cbs.dtu.dk/services/KmerResistance/ | It provides resistome profiles from whole genome sequence using k-mer approach | March 17, 2020 | Clausen et al., 2018 |
| 9 | AMRFinderPlus | https://www.ncbi.nlm.nih.gov/pathogens/antimicrobial-resistance/AMRFinder/ | It focused on acquired or intrinsic AMR genes through HMM approach. It also detects other class of resistance genes such as heavy metal resistance genes. | May 13 2020 | Feldgarden et al., 2019 |
| 10 | RAST and PATRIC | https://rast.nmpdr.org/ https://patricbrc.org/ | It provides genotypic and phenotype prediction in genomes including the identification of genomic regions relating to ARGs | NA | Davis et al., 2016 |
| 11 | ARG-ANNOT | http://www.mediterranee-infection.com/article.php?laref=282&titer=arg-annot | It detects existing and putative new ARGs in bacterial genomes | Monthly | Gupta et al., 2014 |
| 12 | sraX | https://github.com/lgpdevtools/srax | A fully automated tool for resistome analysis in bacterial genomes. The results are displayed in HTML formatted files. | Feb 5 2020 | Panunzi, 2020 |
| 13 | Abricate | https://github.com/tseemann/abricate | In scans contigs for antimicrobial resistance or virulence genes. However, it does not resistance due to point detect mutations. | Mar 28 2020 | Zong et al., 2018 |
| 14 | Search Engine for Antimicrobial Resistance | http://computing.bio.cam.ac.uk/sear/SEAR_WEB_PAGE/SEAR.html | A web based tool for detection of horizontally acquired ARGs from raw metagenomic reads | NA | Rowe et al., 2015 |
| 15 | Sequence-Search-Tool-for-Antimicrobial-Resistance-(SSTAR) | https://github.com/tomdeman-bio/Sequence-Search-Tool-for-Antimicrobial-Resistance-SSTAR- | A standalone software written in java (hence platform independent) that predicts ARGs from WGS. It also notifies users if it detects a truncate a possible ARG. | Sep 11, 2019 | de Man and Limbago, 2016 |
| 16 | MEGARes | https://github.com/cdeanj/resistomeanalyzer | A database that includes ARGs as well as biocide and heavy metal resistance genes | Aug 1, 2018 | Lakin et al., 2017 |
| 17 | Multiple Antibiotic Resistance Annotator (MARA) | http://mara.spokade.com | Multiple Antibiotic Resistance Annotator (MARA) database is mainly focused on the gram negative mobile ARGs | NA | Partridge and Tsafnat, 2018 |
| 18 | FARME DB | http://staff.washington.edu/jwallace/farme | Functional Antibiotic Resistant Metagenomic Element (FARME) database focus on the mobile elements are the flanking genes | NA | Wallace et al., 2017 |
| 19 | ARGA | http://mem.rcees.ac.cn:8083/ | It consists of a database of antibiotic resistance gene with the main focus on ARG primer designing | Mar 25th, 2019 | Wei et al., 2019 |
| 20 | ARGminer | http://bench.cs.vt.edu/argminer | An online platform that enables curation of ARGs through crowdsourcing | NA | Arango-Argoty et al., 2020 |
| 21 | ResistoMap | http://resistomap.rcpcm.org/ | An interactive web based tool for visualization of ARGs in human gut micorbiome | NA | Yarygin et al., 2017 |
| 22 | ARGs-OSP | http://args-osp.herokuapp.com | ARGs-OSP (antibiotic resistant genes-online searching platform) is an online ARG search platform with over 50 thousand WGS and more than 800 metagenoms | NA | Zhang et al., 2020 |
| 23 | LRE-Finder | https://cge.cbs.dtu.dk/services/LRE-finder/ | A web tool to study the mutation in 23S rRNA gene and linezolid resistance using whole-genome sequence data. | NA | Hasman et al., 2019 |
| 24 | MvirDB | http://mvirdb.llnl.gov/ | It is a database of antibiotic resistance gene along with protein toxins and virulence factor | NA | Zhou et al., 2007 |
| 25 | MUBII-TB-DB | http://umr5558-bibiserv.univ-lyon1.fr/mubii/mubii-select.cgi | A database of mutations that confer resistance to ARGs in Mycobacterium tuberculosis | NA | Flandrois et al., 2014 |