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Transposons mobility in M. incognita (INRA - Institut National de la Recherche Agronomique)
Mobility of transposable elements across different isolates of the root-knot nematode M. incognita.
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application/octet-stream - 15.0 KB - MD5: a289e7b2ac27cf677d3bb17c88473a6e
gene analysis workflow used to evaluate genes expression and to find genes potentially involved in the TEs transposition machinery.
text/plain - 7.3 KB - MD5: f32e11c63eafc5d7634c0d7f67002959
List of genes (ID) with both TE-related domains and non-TE related domains. Produced by get_genes_list_from_hmmer_output.py
text/plain - 31.5 KB - MD5: d6d46ec2de1791978c8f0d6e19161bf3
List of genes with only TE-related domains. Produced by get_genes_list_from_hmmer_output.py
text/plain - 393.8 KB - MD5: 5e2a585d175d38ca742ee07d9888eab7
List of genes with no TE-related domains. Produced by get_genes_list_from_hmmer_output.py
text/plain - 38.8 KB - MD5: 68bb753f9425f07f36312dd223c5bf1d
Concatenation of the genes ID list contained in genesWithBothTypesOfDomains.minc_v3.txt and genesWithOnlyTErelatedDomains.minc_v3.txt
text/x-python - 20.9 KB - MD5: a24db3926c74a0d8fbaffe461ab0f2e1
In-house python (>=3) scripts which take as input HMMER3 output (tabular format) and extract the best HMM profiles chain for each protein. Requires the following libraries: sys, os, csv, re, pandas
text/x-python - 2.1 KB - MD5: 4e7a2f0cf78643701e5ed0b606d3ce21
In-house python (>=3) scripts which create gene list from get_genes_domains_from_hmmer3_output.py output. Requires the following libraries: sys, os
application/octet-stream - 1.4 GB - MD5: f6c227cb747976c695ba7f3a6303fb98
hmm profiles database made from the concatenation of pfam32 and GyDB2. Used to identify protein coding genes with TE related domains.
text/plain - 3.2 MB - MD5: 80cea844a986fd903a0dfe48a238af9f
data from a previously published life-stage specific RNA-seq analysis of M. incognita transcriptome during tomato plant infection (Blanc-Mathieu et al. 2017). This analysis encompassed four different life stages: (i) eggs, (ii) pre-parasitic second stage juveniles (J2), (iii)...
application/octet-stream - 14.7 MB - MD5: 1901ea90b65d48ad8e88af5cf298d506
M. incognita proteome stem from https://doi.org/10.1371/journal.pgen.1006777
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