Johann Confais

@[email protected]
34 Followers
53 Following
8 Posts
Bioinformatics @INRAE_URGI
Interested in #Genomics, #Evolution, #Transposons, #TransposableElement, #Pangenomic
Ici depuis24 nov. 2022
Show threadJohann ConfaisJan 10, 2023
The Pfam (@PfamDB) & GyDB HMM profiles bank formatted for #REPET is available on @INRAE_URGI website : https://urgi.versailles.inrae.fr/download/repet/profiles/ProfilesBankForREPET_Pfam35.0_GypsyDB.hmm.tar.gz 4/4
Show threadJohann ConfaisJan 10, 2023
The REXdb release Viridiplantae v3.0 (@MacasLab) #database for #Transposons, covering > 13,000 gypsy/copia elements from major groups of green plants formatted for #REPET is available on @INRAE_URGI website : https://urgi.versailles.inrae.fr/download/repet/banks/REXdb/Viridiplantae_v3.0_ALL_protein-domains_repet_formated.fsa
https://doi.org/10.1186/s13100-018-0144-1 3/4
Show threadJohann ConfaisJan 10, 2023
The Dfam release 3.6 (@isbsci) #database for #Transposons, covering > 700,000 TE families including > 18,000 curated families over > 1000 species formatted for #REPET is available on @INRAE_URGI website : https://urgi.versailles.inrae.fr/download/repet/banks/dfam/
https://doi.org/10.1186/s13100-020-00230-y 2/4
Index of /download/repet/banks/dfam

Johann ConfaisJan 10, 2023
📢 Hey REPET users ! To improve the classification of your #Transposons reference library there are new banks formatted for #REPET available on @INRAE_URGI
website : https://urgi.versailles.inra.fr/Tools/REPET. #TEHub🧵⬇️1/4
REPET - URGI

Content Management System

Johann ConfaisJan 10, 2023
INRAE_URGIJan 6, 2023
The genome annotation service of the plant bioinformatics facility #PlantBioinfoPF is proud to be funded by @GIS_IBiSA
to further improve the distribution and reproducibility of REPET package.
@michaelalaux
@JohannConfais
@Bioinf0mics
Johann ConfaisJan 10, 2023
Vandepoele labJan 10, 2023
Stats PLAZA plant comparative genomics platform 2022: 19k unique users, 437k page views, average session duration: 10 min. Thanks to all users for support/feedback.
Johann ConfaisJan 10, 2023
Show threadVandepoele labJan 10, 2023
New to the PLAZA platform? Check out our Publications, Documentation, Workshop course material and more here: https://bioinformatics.psb.ugent.be/plaza/documentation
Documentation

Johann ConfaisDec 1, 2022
Francois SabotDec 1, 2022
RT @pangenomepapers
A Pangenome Approach to Detect and Genotype TE Insertion Polymorphisms http://dlvr.it/SddSXC
A Pangenome Approach to Detect and Genotype TE Insertion Polymorphisms - PubMed

Pangenome graphs are flexible data structures that contain the genetic variation that exists in a population of genomes and describe the sequences of the many possible ensuing haplotypes. Here, we use such a pangenome graph to represent and genotype transposable element (TE) polymorphisms. By combin …

PubMed