Detection of horizontal sequence transfer in microorganisms in the genomic era
TALL, M. L.; Mbogning Fonkou, M. d.; KUETE YIMAGOU, E.; RAOULT, D.; LEVASSEUR, A.
Show abstract
Sequence transfer and genome remodeling are very frequent events in microorganisms, especially prokaryotes. This is due to the mosaic structure of the genomes, which calls into question the correct classification of genomes in terms of a single gene or a group of genes. We started here, as a first step, the inventory of bioinformatics tools applied to the detection of horizontal sequence transfers in microorganisms in the genomic era by applying bibliometric survey. Our bibliographic analysis allowed us to identify 17 main tools for the detection of chimeras. The first Bellerophon developed in 2004, followed by CCode and Pintail in 2005; Mallard in 2006; Mothur in 2009; Blackbox Chimera in 2010; Perseus, ChimeraSlayer, UCHIME 1 and UCHIME2, and ChimeraScan in 2011; Decipher in 2012; EBARDenovo and FunFrame in 2013; CATCh in 2015; Uchime 2 in 2016 and ChimeraMiner in April 2019. We then described each of these tools, highlighting their operating principles as well as the advantages and limitations of each (specificities, sensitivity, rapidity and frequent updates). The number of articles citing these tools has increased over the years especially for Mothur, Uchime, VSEARCH and ChimeraSlayer, thus demonstrating the interest of researchers in these tools and the need to decipher chimeras in genomic era.
Matching journals
The top 7 journals account for 50% of the predicted probability mass.
Similar papers in this journal
- Investigating Antimicrobial Resistance Genes in Kenya, Uganda and Tanzania Cattle Using Metagenomics 94%
- DnoisE: Distance denoising by Entropy. An open-source parallelizable alternative for denoising sequence datasets 94%
- StrainFLAIR: Strain-level profiling of metagenomic samples using variation graphs 94%
Similar papers in this journal
- Omnicrobe, an open-access database of microbial habitats and phenotypes using a comprehensive text mining and data fusion approach 96%
- Comparative evaluation of bioinformatic tools for virus-host prediction and their application to a highly diverse community in the Cuatro Cienegas Basin, Mexico 94%
- BC-store: a program for mgiseq barcode sets analysis 94%
Similar papers in this journal
- Comprehensive benchmarking of metagenomic classification tools for long-read sequencing data 96%
- Natrix: A Snakemake-based workflow for processing, clustering, and taxonomically assigning amplicon sequencing reads 95%
- Ribovore: ribosomal RNA sequence analysis for GenBank submissions and database curation 95%
Similar papers in this journal
- Interpretations of microbial community studies are biased by the selected 16S rRNA gene amplicon sequencing pipeline. 94%
- BacAnt: A Combination Annotation Server for Bacterial DNA Sequences to Identify Antibiotic Resistance Genes, Integrons, and Transposable Elements. 93%
- Using QC-Blind for quality control and contamination screening of bacteria DNA sequencing data without reference genome 93%
Similar papers in this journal
- No one tool to rule them all: Prokaryotic gene prediction tool performance is highly dependent on the organism of study 95%
- ganon: precise metagenomics classification against large and up-to-date sets of reference sequences 94%
- Megan Server: facilitating interactive access to metagenomic data on a server 94%
"Similar papers" are the closest papers from that journal in the model's embedding space. They show what the match is built on, but the ranking comes mostly from a classifier over the whole training set, not from these examples alone.