UMR DIADE

DIversity - Adaptation - plant DEvelopment

The DIADE Research Unit aims to understand the diversification of tropical plants, one of the main original reservoirs of biodiversity, and for which conservation, management and exploitation are an important issue for Sustainable Development.

The nine teams forming the Unit belong to IRD, University of Montpellier, CIRAD, and CNRS.

CERES Team

DYNADIV Team

EVOGEC Team

ADvENS Team

AgroLD

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11 to 20 of 962 Results

chm13.draft_v1.1_chr1.fasta Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 240.8 MB - MD5: ab2421da8b88a867d087c3f452a6969f Fasta file of the chromosome 1 of the genome CHM13,from https://projects.ensembl.org/hprc/.
EcoliGraph_MGC.gfa Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 112.8 MB - MD5: e5183acfb527fcd7b01ac4386d7be290 Data E.coli pangenome graph built with 12 genomes from the paper available at http://dx.doi.org/10.7554/eLife.78834.
feature_types.txt Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Plain Text - 638 B - MD5: 571dcfb312543edd81dca0524212459a Lists all the feature types in the human annotation (CHM13_chr1.gff), necessary to run Liftoff on all the features.
feature_types.txt Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Plain Text - 104 B - MD5: 6752a18a92500cff53d9d8c4210fc1bc Data Lists all the feature types in the E.coli annotation (sequence_filter_rename_K_12_MG1655_09949b0.gff3), necessary to run Liftoff on all the features.
GCA_000001405.15_GRCh38_chr1.fna Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 240.8 MB - MD5: 90780be24a8555613e6ad0bd2f8a0935 Data Fasta file of the chromosome 1 of the genome GRCh38,from https://projects.ensembl.org/hprc/.
IRGSP_nipponbare.fasta Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 363.7 MB - MD5: e923ca38bac7f347ffbf88142b93428f Fasta file of the genome Nipponbare, from the paper from 2013 by Kawahara, Y., de la Bastide, M., Hamilton, J.P. et al., "Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data" (doi:10.1186/1939-8433-6-4).
IRGSP_nipponbare.genome Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 539 B - MD5: 562caffe11637996021726b3d3a2e59b Data Text file necessary to run VG on the rice data.
K_12_MG1655_09949b0.fasta Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 4.5 MB - MD5: 4e617b3e53fbe61f2ca689dda227a674 Data Fasta file of the genome K_12_MG1655_09949b0, from the paper available at http://dx.doi.org/10.7554/eLife.78834.
nb_allFeatures.fa Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 626.5 MB - MD5: 25854fb0391bc1676dcddc967fdf3371 Data Fasta file of all the features from the annotation file "nb_allFeatures.gff3".
nb_allFeatures.gff3 Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper Unknown - 77.7 MB - MD5: 4a8e0be436e73bdf85baa362947c6dba Data Annotation file of the genome Nipponbare from the Rice Genome Annotation Project, available at https://rice.uga.edu/.

chm13.draft_v1.1_chr1.fasta

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 240.8 MB -

Fasta file of the chromosome 1 of the genome CHM13,from https://projects.ensembl.org/hprc/.

EcoliGraph_MGC.gfa

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 112.8 MB -

Data

E.coli pangenome graph built with 12 genomes from the paper available at http://dx.doi.org/10.7554/eLife.78834.

feature_types.txt

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Plain Text - 638 B -

Lists all the feature types in the human annotation (CHM13_chr1.gff), necessary to run Liftoff on all the features.

feature_types.txt

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Plain Text - 104 B -

Data

Lists all the feature types in the E.coli annotation (sequence_filter_rename_K_12_MG1655_09949b0.gff3), necessary to run Liftoff on all the features.

GCA_000001405.15_GRCh38_chr1.fna

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 240.8 MB -

Data

Fasta file of the chromosome 1 of the genome GRCh38,from https://projects.ensembl.org/hprc/.

IRGSP_nipponbare.fasta

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 363.7 MB -

Fasta file of the genome Nipponbare, from the paper from 2013 by Kawahara, Y., de la Bastide, M., Hamilton, J.P. et al., "Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data" (doi:10.1186/1939-8433-6-4).

IRGSP_nipponbare.genome

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 539 B -

Data

Text file necessary to run VG on the rice data.

K_12_MG1655_09949b0.fasta

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 4.5 MB -

Data

Fasta file of the genome K_12_MG1655_09949b0, from the paper available at http://dx.doi.org/10.7554/eLife.78834.

nb_allFeatures.fa

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 626.5 MB -

Data

Fasta file of all the features from the annotation file "nb_allFeatures.gff3".

nb_allFeatures.gff3

Mar 10, 2025 - Data used for the analysis described in GrAnnoT paper

Unknown - 77.7 MB -

Data

Annotation file of the genome Nipponbare from the Rice Genome Annotation Project, available at https://rice.uga.edu/.

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