Biology subjects

Touzet, H.

Publications and source records attributed to Touzet, H..

8 recordsLinked to original sources

bioRxiv2025

RNA-tailor: accurate gene-level identification of transcript isoform diversity from long reads

Accurate splicing isoform identification is an essential need for progress of modern medicine and biological knowledge. The advent of long-read sequencing technologies opened up the possibility of sequencing full length transcripts. Most of the existing methods aims to predict isoforms at genome scale. However, solving all isoforms at genome scale is not always needed, mostly when one is interested in a single gene or a few genes. It also brings algorithmic constraints, encouraging the use of less accurate alignment algorithms and downgrading sensitivity of methods to determine the repertoire of isoforms. The aim of RNA-tailor is to make available an easy-to-use tool to perform single gene resolution of alternative splicing isoform repertoire with high accuracy. To leverage such precision, RNA-tailor uses a combination of exact alignment algorithm and context aware alignment corrections. By analyzing both real and simulated datasets, we show that RNA-tailor is able to achieve higher sensitivity.

bioinformatics↗

bioRxiv2025

PAMPA: a software for peptide markers and taxonomic identification for ZooMS samples in Archaeology and Paleontology

ZooMS (Zooarchaeology by Mass Spectrometry) offers a rapid and cost-effective method for species identification of animal remains through peptide mass fingerprinting. After mass spectrum generation, a mostly used way to perform taxonomic identification is to compare the mass fingerprints to a reference database of diagnostic peptide markers to determine the species of origin. This analytical stage, however, is tedious and error-prone, often necessitating manual examination of spectra. In this paper, we present a comprehensive approach to automate and standardize the usage of peptide markers and the classification of ZooMS spectra. We have developed a software called PAMPA (Protein Analysis by Mass Spectrometry for Ancient Species), for which we demonstrate the effectiveness using a variety of spectral data from bone samples generated by MALDI-TOF and MALDI-FTICR. PAMPA is open-source and comes with a database of peptide markers and collection of curated COL1A1 and COL1A2 sequences. We believe it will be a valuable resource for the scientific community.

bioinformatics↗

bioRxiv2023

Automated evaluation of multiple sequence alignment methods to handle third generation sequencing errors

Most third-generation sequencing (TGS) processing tools rely on multiple sequence alignment (MSA) methods to manage sequencing errors. Despite the broad range of MSA approaches available, a limited selection of implementations are commonly used in practice for this type of application, and no comprehensive comparative assessment of existing tools has been under-taken to date. In this context, we have developed an automatic pipeline, named MSA_Limit, designed to facilitate the execution and evaluation of diverse MSA methods across a spectrum of conditions representative of TGS reads. MSA_Limit offers insights into alignment accuracy, time efficiency, and memory utilization. It serves as a valuable resource for both users and developers, aiding in the assessment of algorithmic performance and assisting users in selecting the most appropriate tool for their specific experimental settings. Through a series of experiments using real and simulated data, we demonstrate the value of such exploration. Our findings reveal that in certain scenarios, popular methods may not consistently exhibit optimal efficiency and that the choice of the most effective method varies depending on factors such as sequencing depth, genome characteristics, and read error patterns. MSA_Limit is open source is freely available at gitlab.cristal.univ-lille.fr/crohmer/msa-limit and all presented results and necessary information to reproduce the experiments are available at gitlab.cristal.univ-lille.fr/crohmer/msa-limit

bioinformatics↗

bioRxiv2022

Porechop_ABI: discovering unknown adapters in ONT sequencing reads for downstream trimming

MotivationOxford Nanopore Technologies (ONT) sequencing has become very popular over the past few years and offers a cost-effective solution for many genomic and transcriptomic projects. One distinctive feature of the technology is that the protocol includes ligation of adapters to both ends of each fragment. Those adapters should then be removed before downstream analyses, either during the basecalling step or by explicit trimming. This basic task may be tricky when the definition of the adapter sequence is not well-documented. ResultsWe have developed a new method to scan a set of ONT reads to see if it contains adapters, without any prior knowledge on the sequence of the potential adapters, and then trim out those adapters. The algorithm is based on approximate k-mers and is able to discover adapter sequences based on their frequency alone. The method was successfully tested on a variety of ONT datasets with different flowcells, sequencing kits and basecallers. AvailabilityThe resulting software, named Porechop_ABI, is open-source and is available at https://github.com/bonsai-team/Porechop_ABI.

bioinformatics↗

bioRxiv2020

Substitution of nucleotide-sugar by trehalose-dependent glycogen synthesis pathways in Chlamydiales underlines an unusual requirement for storage polysaccharides within obligate intracellular bacteria

All obligate intracellular pathogens or symbionts of eukaryotes lack glycogen metabolism. Most members of the Chlamydiales order are exceptions to this rule as they contain the classical GlgA-GlgC-dependent pathway of glycogen metabolism that relies on the ADP-Glucose substrate. We surveyed the diversity of Chlamydiales and found glycogen metabolism to be universally present with the important exception of Criblamydiaceae and Waddliaceae families that had been previously reported to lack an active pathway. However, we now find elements of the more recently described GlgE maltose-1-P-dependent pathway in several protist-infecting Chlamydiales. In the case of Waddliaceae and Criblamydiaceae, the substitution of the classical pathway by this recently proposed GlgE pathway was essentially complete as evidenced by the loss of both GlgA and GlgC. Biochemical analysis of recombinant proteins expressed from Waddlia chondrophila and Estrella lausannensis established that both enzymes do polymerize glycogen from trehalose through the production of maltose-1-P by TreS-Mak and its incorporation into glycogens outer chains by GlgE. Unlike Mycobacteriaceae where GlgE-dependent polymerization is produced from both bacterial ADP-Glc and trehalose, glycogen synthesis seems to be entirely dependent on host supplied UDP-Glc and Glucose-6-P or on host supplied trehalose and maltooligosaccharides. These results are discussed in the light of a possible effector nature of these enzymes, of the chlamydial host specificity and of a possible function of glycogen in extracellular survival and infectivity of the chlamydial elementary bodies. They underline that contrarily to all other obligate intracellular bacteria, glycogen metabolism is indeed central to chlamydial replication and maintenance.

microbiology↗

bioRxiv2020

A single master regulator controls asexual cell cycle division patterns in Toxoplasma gondii

All apicomplexan parasites have complex life cycles exhibiting division characterized by a tightly regulated cell cycle control, resulting in the emergence of daughter parasites in possession of a single nucleus and a complete set of organelles. Apicomplexa have evolved efficient and distinctive strategies for intracellular replication where the timing of emergence of the daughter cells, a process termed "budding", is a decisive element. However, the molecular mechanisms that provide the proper timing of parasite budding remain unknown. Using Toxoplasma gondii as a model Apicomplexa, we identified a master regulator that controls the timing of the budding process. We show that an ApiAP2 transcription factor, TgAP2IX-5, controls cell cycle events downstream of centrosome duplication including organelle division and segregation. TgAP2IX-5 binds to the promoter of hundreds of genes and controls the activation of the budding-specific cell cycle expression program. We show that TgAP2IX-5 regulates the expression of specific transcription factors that are necessary for the completion of the budding cycle. TgAP2IX-5 acts as a licensing factor that ensures that asexual proliferation continues by promoting the inhibition of the differentiation pathway at each round of the cell cycle. Therefore, TgAP2IX-5 is a master regulator that controls both cell cycle and developmental pathways.

microbiology↗

bioRxiv2018

Comparative assessment of long-read error-correction software applied to RNA-sequencing data

MotivationLong-read sequencing technologies offer promising alternatives to high-throughput short read sequencing, especially in the context of RNA-sequencing. However these technologies are currently hindered by high error rates that affect analyses such as the identification of isoforms, exon boundaries, open reading frames, and the creation of gene catalogues. Due to the novelty of such data, computational methods are still actively being developed and options for the error-correction of RNA-sequencing long reads remain limited.\n\nResultsIn this article, we evaluate the extent to which existing long-read DNA error correction methods are capable of correcting cDNA Nanopore reads. We provide an automatic and extensive benchmark tool that not only reports classical error-correction metrics but also the effect of correction on gene families, isoform diversity, bias toward the major isoform, and splice site detection. We find that long read error-correction tools that were originally developed for DNA are also suitable for the correction of RNA-sequencing data, especially in terms of increasing base-pair accuracy. Yet investigators should be warned that the correction process perturbs gene family sizes and isoform diversity. This work provides guidelines on which (or whether) error-correction tools should be used, depending on the application type.\n\nBenchmarking softwarehttps://gitlab.com/leoisl/LR_EC_analyser

bioinformatics↗

bioRxiv2017

MATAM: Reconstruction Of Phylogenetic Marker Genes From Short Sequencing Reads In Metagenomes

MotivationAdvances in the sequencing of uncultured environmental samples, dubbed metagenomics, raise a growing need for accurate taxonomic assignment. Accurate identification of organisms present within a community is essential to understanding even the most elementary ecosystems. However, current high-throughput sequencing technologies generate short reads which partially cover full-length marker genes and this poses difficult bioinformatic challenges for taxonomy identification at high resolution\n\nResultsWe designed MATAM, a software dedicated to the fast and accurate targeted assembly of short reads sequenced from a genomic marker of interest. The method implements a stepwise process based on construction and analysis of a read overlap graph. It is applied to the assembly of 16S rRNA markers and is validated on simulated, synthetic and genuine metagenomes. We show that MATAM outperforms other available methods in terms of low error rates and recovered genome fractions and is suitable to provide improved assemblies for precise taxonomic assignments.\n\nAvailabilityhttps://github.com/bonsai-team/matam\n\nContactpierre.pericard@gmail.com, helene.touzet@univ-lille1.fr

bioinformatics↗