MareyMap online: A user-friendly web application and database service for estimating recombination rates using physical and genetic maps

Given the importance of meiotic recombination in biology, there is a need to develop robust methods to estimate meiotic recombination rates. A popular approach, called the Marey map approach, relies on comparing genetic and physical maps of a chromosome to estimate local recombination rates. In the past, we have implemented this approach in an R package called MareyMap, which includes many functionalities useful to get reliable recombination rate estimates in a semi-automated way. MareyMap has been used repeatedly in studies looking at the effect of recombination on genome evolution. Here, we propose a simpler user-friendly web service version of MareyMap, called MareyMap Online, which allows a user to get recombination rates from her/his own data or from a publicly available database that we offer in a few clicks. When the analysis is done, the user is asked whether her/his curated data can be placed in the database and shared with other users, which we hope will make meta-analysis on recombination rates including many species easy in the future

Capturing Auxin Response Factors Syntax Using DNA Binding Models

International audienceAuxin is a key hormone performing a wealth of functions throughout the life cycle of plants. It acts largely by regulating genes at the transcriptional level through a family of transcription factors called auxin response factors (ARFs). Even though all ARF monomers analyzed so far bind a similar DNA sequence, there is evidence that ARFs differ in their target genomic regions and regulated genes. Here, we report the use of position weight matrices (PWMs) to model ARF DNA binding specificity based on published DNA affinity purification sequencing (DAP-seq) data. We found that the genome binding of two ARFs (ARF2 and ARF5/Monopteros [MP]) differ largely because these two factors have different preferred ARF binding site (ARFbs) arrangements (orientation and spacing). We illustrated why PWMs are more versatile to reliably identify ARFbs than the widely used consensus sequences and demonstrated their power with biochemical experiments in the identification of the regulatory regions of IAA19, an well-characterized auxin-responsive gene. Finally, we combined gene regulation by auxin with ARF-bound regions and identified specific ARFbs configurations that are over-represented in auxin-upregulated genes, thus deciphering the ARFbs syntax functional for regulation. Our study provides a general method to exploit the potential of genome-wide DNA binding assays and to decode gene regulation

JASPAR 2018: update of the open-access database of transcription factor binding profiles and its web framework

International audienceJASPAR (http://jaspar.genereg.net) is an open-access database of curated, non-redundant transcription factor (TF)-binding profiles stored as position frequency matrices (PFMs) and TF flexible models (TFFMs) for TFs across multiple species in six tax-onomic groups. In the 2018 release of JASPAR, the CORE collection has been expanded with 322 new PFMs (60 for vertebrates and 262 for plants) and 33 PFMs were updated (24 for vertebrates, 8 for plants and 1 for insects). These new profiles represent a 30% expansion compared to the 2016 release. In addition , we have introduced 316 TFFMs (95 for vertebrates , 218 for plants and 3 for insects). This release incorporates clusters of similar PFMs in each taxon and each TF class per taxon. The JASPAR 2018 CORE vertebrate collection of PFMs was used to predict TF-binding sites in the human genome. The predictions are made available to the scientific community through a UCSC Genome Browser track data hub. Finally , this update comes with a new web framework with an interactive and responsive user-interface, along with new features. All the underlying data can be retrieved programmatically using a RESTful API and through the JASPAR 2018 R/Bioconductor package

Divers ouvrages de mathématiques et de physique , par Messieurs de l'Académie royale des sciences

Comprend : De crassitia et viribus tuborum in aquaeductibus secundum diversas fontium altitudines diversasque tuborum diametros. - Experimenta circa altitudines et amplitudines projectionis corporum gravium, instituta cum argento vivo a D. Romer ; Du micromètre [et aussi, dans les Divers ouvrages de M. Picard, Mesures prises sur les originaux et comparées avec le pied du Chastelet de Paris, par M. Auzout] ; Méthode pour trouver la solution des problèmes par les exclusions. Abrégé des combinaisons, par M. de Frénicle. [- Des Quarrez magiques...] ; Divers ouvrages de M. de Roberval. [Observations sur la composition des mouvements... - Projet d'un livre de mécanique traitant des mouvements composés. - De Recognitione aequationum. - De Geometrica planarum et cubicarum aequationum resolutione. - Traité des indivisibles. - De Trochoïde ejusque spatio. - Epistola... ad R. P. Mersennum. - Epistola... ad Evangelistam Toricellum] ; Divers ouvrages de M. Hugens de Zulichem. [De la Cause de la pesanteur. - Démonstration de l'équilibre de la balance. - De Potentiis fila funesve trabentibus. - Nouvelle force mouvante par le moyen de la poudre à canon et de l'air. - Constructio loci ad hyperbolam per asymptotos. - Demonstratio regulae de maximis et minimis. - Regula ad inveniendas tangentes curvarum. - Construction d'un problème d'optique] ; Epistola... ad Robervallium. [Florentiae, Kal. octob. 1643] ; Règles pour les jets d'eau... ; Divers ouvrages de M. Picard. [De la pratique des grands cadrans par le calcul. - "De mensuris". - Fragmens de dioptrique]Contient une table des matièresAvec mode text