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Type: (datasets) Kind of Data: Text

21 to 30 of 62 Results

M. incognita predicted secreted proteins 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...
Global statistics of the orthofinder analysis Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA Danchin, Etienne; Grynberg, Priscila; Togawa, Roberto, 2020, "Global statistics of the orthofinder analysis", https://doi.org/10.15454/ZGUP7N, Portail Data INRAE, V1 General statistics of the orhofinder analysis on the 63 species (including 61 nematodes). Number of orthogroups, of genes in orthogroups etc...
Orthofinder rooted species tree Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA Danchin, Etienne; Grynberg, Priscila; Togawa, Roberto, 2020, "Orthofinder rooted species tree", https://doi.org/10.15454/MBMOQC, Portail Data INRAE, V1 Rooted phylogenomics species tree performed by Orthofinder on the 63 species, in Newick format. An annotated version of the tree in PDF format, produced with iTOL is also available.
Annotated list of species used in this study Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA Danchin, Etienne; Grynberg, Priscila; Togawa, Roberto, 2020, "Annotated list of species used in this study", https://doi.org/10.15454/IIAQOW, Portail Data INRAE, V1 Annotated list of the 63 species used in the Orthofinder comparative analysis of nematodes (61 species) and two tardigrade species as out-groups. Description: Lines 1-64, definition of columns - Abbrev Species: abbreviated species name. Species identifiers used in all the Orthofi...
M. incognita candidate effector proteins Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA Danchin, Etienne, 2020, "M. incognita candidate effector proteins", https://doi.org/10.15454/CSTXU2, Portail Data INRAE, V1 Accession numbers of M. incognita candidate effectors. These proteins are predicted to be secreted based on the presence of a signal peptide for secretion and absence of transmembrane domains. Furthermore at least one motif known to be enriched in effector proteins is present in...
MERCI effector-enriched motifs in the 100 first amino acids of M. incognita proteins 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)
PPN-specific M. incognita proteins with no hits against NR Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA Danchin, Etienne, 2020, "PPN-specific M. incognita proteins with no hits against NR", https://doi.org/10.15454/48436V, Portail Data INRAE, V1 Accession numbers of M. incognita proteins specific to plant-parasitic nematodes as determined by the orthofinder analysis and returning no significant hits against the NCBI's NR according to Diamond.
Taxonomic distribution of M. incognita Diamond hits against the NCBI's nr library Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA Danchin, Etienne; Rancurel, Corinne; Togawa, Roberto, 2020, "Taxonomic distribution of M. incognita Diamond hits against the NCBI's nr library", https://doi.org/10.15454/FROF42, Portail Data INRAE, V1 Taxonomic distribution of M. incognita Diamond hits against the NCBI's nr library. The taxonomy has been determined by Diamond LCA algorithm via outformat 102. Two reports are available: 1- all the M. incognita proteins as queries 2- PPN-specific M. incognita proteins as queries...
M. incongnita proteins specific to plant-parasitic nemaotdes 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.
Horizontal gene transfer candidates in M. incognita Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA Danchin, Etienne; Rancurel, Corinne, 2020, "Horizontal gene transfer candidates in M. incognita", https://doi.org/10.15454/W6SWZH, Portail Data INRAE, V1, UNF:6:wuWOjB++Puk5yJOSrDfxWw== [fileUNF] Analysis of horizontal gene transfer (HGT) candidates on the M. incognita predicted proteins from (Blanc-Mathieu et al. 2017), using Alienness (Rancurel et al. 2017) on a Diamond search against the NCBI's nr library. The following parameters were used in Alienness Taxonomic group...

M. incognita predicted secreted proteins

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...

Global statistics of the orthofinder analysis

Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA

Danchin, Etienne; Grynberg, Priscila; Togawa, Roberto, 2020, "Global statistics of the orthofinder analysis", https://doi.org/10.15454/ZGUP7N, Portail Data INRAE, V1

General statistics of the orhofinder analysis on the 63 species (including 61 nematodes). Number of orthogroups, of genes in orthogroups etc...

Orthofinder rooted species tree

Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA

Danchin, Etienne; Grynberg, Priscila; Togawa, Roberto, 2020, "Orthofinder rooted species tree", https://doi.org/10.15454/MBMOQC, Portail Data INRAE, V1

Rooted phylogenomics species tree performed by Orthofinder on the 63 species, in Newick format. An annotated version of the tree in PDF format, produced with iTOL is also available.

Annotated list of species used in this study

Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA

Danchin, Etienne; Grynberg, Priscila; Togawa, Roberto, 2020, "Annotated list of species used in this study", https://doi.org/10.15454/IIAQOW, Portail Data INRAE, V1

Annotated list of the 63 species used in the Orthofinder comparative analysis of nematodes (61 species) and two tardigrade species as out-groups. Description: Lines 1-64, definition of columns - Abbrev Species: abbreviated species name. Species identifiers used in all the Orthofi...

M. incognita candidate effector proteins

Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA

Danchin, Etienne, 2020, "M. incognita candidate effector proteins", https://doi.org/10.15454/CSTXU2, Portail Data INRAE, V1

Accession numbers of M. incognita candidate effectors. These proteins are predicted to be secreted based on the presence of a signal peptide for secretion and absence of transmembrane domains. Furthermore at least one motif known to be enriched in effector proteins is present in...

MERCI effector-enriched motifs in the 100 first amino acids of M. incognita proteins

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)

PPN-specific M. incognita proteins with no hits against NR

Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA

Danchin, Etienne, 2020, "PPN-specific M. incognita proteins with no hits against NR", https://doi.org/10.15454/48436V, Portail Data INRAE, V1

Accession numbers of M. incognita proteins specific to plant-parasitic nematodes as determined by the orthofinder analysis and returning no significant hits against the NCBI's NR according to Diamond.

Taxonomic distribution of M. incognita Diamond hits against the NCBI's nr library

Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA

Danchin, Etienne; Rancurel, Corinne; Togawa, Roberto, 2020, "Taxonomic distribution of M. incognita Diamond hits against the NCBI's nr library", https://doi.org/10.15454/FROF42, Portail Data INRAE, V1

Taxonomic distribution of M. incognita Diamond hits against the NCBI's nr library. The taxonomy has been determined by Diamond LCA algorithm via outformat 102. Two reports are available: 1- all the M. incognita proteins as queries 2- PPN-specific M. incognita proteins as queries...

M. incongnita proteins specific to plant-parasitic nemaotdes

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.

Horizontal gene transfer candidates in M. incognita

Aug 18, 2020 - Genes specific to phytoparasitic nematodes INRAE/EMBRAPA

Danchin, Etienne; Rancurel, Corinne, 2020, "Horizontal gene transfer candidates in M. incognita", https://doi.org/10.15454/W6SWZH, Portail Data INRAE, V1, UNF:6:wuWOjB++Puk5yJOSrDfxWw== [fileUNF]

Analysis of horizontal gene transfer (HGT) candidates on the M. incognita predicted proteins from (Blanc-Mathieu et al. 2017), using Alienness (Rancurel et al. 2017) on a Diamond search against the NCBI's nr library. The following parameters were used in Alienness Taxonomic group...

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