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31 to 40 of 74 Results
Aug 5, 2020
Ehrenmann, Francois; Plomion, Christophe, 2020, "Oak Genome Sequencing Website", https://doi.org/10.15454/WSMRIN, Portail Data INRAE, V2
The oak genome sequencing website, concerning the sequencing of the oak genome and identification of genes important for the adaptation of forest trees, is a permanent resource by INRAE, available at http://www.oakgenome.fr/. It provides access to various resources : oak genome b...
Sep 17, 2019 - EPGV
Toda, Nicholas, 2019, "NLGenomeSweeper", https://doi.org/10.15454/DS6VIK, Portail Data INRAE, V1
NLGenomeSweeper is a command line bash pipeline that searches a genome for NBS-LRR (NLR) disease resistance genes based on the presence of the NB-ARC domain using the consensus sequence of the Pfam HMM profile (PF00931) and class specific consensus sequences built from Vitis vini...
Sep 23, 2019 - Genetic Resources Dataverse
Montarry, Josselin; Esquibet, Magali; Gautier, Camille; Piriou, Christophe; Grenier, Eric; Fournet, Sylvain, 2019, "Microsatellite genotyping of French populations of the carrot cyst nematode Heterodera carotae", https://doi.org/10.15454/MLMDVE, Portail Data INRAE, V1
The dataset include two files containing the genotypic data (Genepop format) for the different Heterodera carotae populations sampled at the plant scale (H_carotae_plants.txt) and at the field scale (H_carotae_fields.txt).
May 14, 2020 - Experimental - Observation - Simulation Dataverse
Laurent, Benoit, 2020, "Microhaplotype genotyping-by-sequencing of 98 highly polymorphic markers in three chestnut tree species", https://doi.org/10.15454/PNBEAM, Portail Data INRAE, V5, UNF:6:vfR+Xz1fRgxgxhqS02yR2g== [fileUNF]
Chestnut species have large ecological, cultural and economic importance. Developing genetic markers for these species is of interest for conservation, breeding or evolutionary studies. We designed 192 primer pairs targeting microsatellites detected in the Castanea mollissima ref...
Jul 25, 2019
Ma, Yuxin; Marais, Armelle; Lefebvre, Marie; Faure, Chantal; Candresse, Thierry, 2019, "Metagenomic analysis of virome cross-talk between cultivated Solanum lycopersicum and wild Solanum nigrum", https://doi.org/10.15454/S486RR, Portail Data INRAE, V1
We selected tomato (Solanum lycopersicum) and european black nightshade (Solanum nigrum) as a pair of related crop-weed species to study the diversity and potential flow of viral populations using high throughput sequencing (HTS) based metagenomics. A total of 20 libraries were p...
Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA
Danchin, Etienne, 2020, "MERCI effector-enriched motifs in the 100 first amino acids of M. incognita proteins", https://doi.org/10.15454/LMY6LV, Portail Data INRAE, V1
MERCI effector-enriched motifs in the 100 first amino acids of M. incognita proteins M. incognita proteins with at least one of the 4 motifs identified as enriched in the known effector proteins as described in (Vens, Rosso, Danchin, Bioinformatics, 2011)
Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA
Danchin, Etienne, 2020, "Meloidogyne incognita Interproscan annotation", https://doi.org/10.15454/9BFFKG, Portail Data INRAE, V1
Interproscan annotation on the 43,718 predicted proteins in the genome of the root-knot nematode Meloidogyne incognita (Blanc-Mathieu et al. 2017, PLoS Genetics). vesrion used: interproscan-5.29-68.0 options used: -dp Disables use of the precalculated match lookup service = all m...
Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA
Danchin, Etienne, 2020, "M. incongnita proteins specific to plant-parasitic nemaotdes", https://doi.org/10.15454/I9MWRS, Portail Data INRAE, V1
Accession numbers of M. incognita predicted proteins having predicted homologs only in other plant-parasitic nematodes (PPN) or being M. incognita-specific.
Jul 3, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA
Danchin, Etienne; Da Rocha, Martine, 2020, "M. incognita protein-coding genes expression patterns", https://doi.org/10.15454/YM2DHE, Portail Data INRAE, V1
M. incognita protein-coding genes expression values across 4 life stages in triplicates. Life stages are as follows: - W: eggs - J2: pre-parasitic infective juveniles - J3: infective juveniles (mic of late J2, J3 and J4) - Fem: adult female Two tables are given, one with the raw...
Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA
Danchin, Etienne, 2020, "M. incognita predicted secreted proteins", https://doi.org/10.15454/JCYZDI, Portail Data INRAE, V1
To identify putative secreted proteins in the M. incognita protein set (Blanc-Mathieu et al. 2017), we searched for predicted signal peptides (SP) for secretion using SignalP v4 (Petersen, Brunak, von Heijne, & Nielsen, 2011). This program improves the differentiation between tra...
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