pPCD-PhylogeneticProfiles.tar.gz

This dataset contains all files necessary to display and explore the pPCD data generated and analysed in the manuscript "Feature architecture-aware ortholog search with fDOG reveals the distribution of plant cell wall-degrading enzymes across life"Software:The data is ready for display with PhyloProfile (https://bioconductor.org/packages/release/bioc/html/PhyloProfile.html)<br>File inventory:1. PCD_seeds-representative.txt - text file comprising the seed protein ids for the 76 representative pPCDs2. README.txt - this file3. cellulase_all.extended.fa - fasta file comprising the amino acid sequences of all orthologs detected for the 235 seed proteins across 18,565 taxa from the three domains of life4. cellulase_all.phyloprofile.valid - Feature architecture aware phylogenetic profiles of 235 pPCDs across 18,565 taxa5. cellulase_all_euks.phyloprofile.valid - Feature architecture aware phylogenetic profiles of 235 pPCDs across 1,354 eukaryotes6. cellulase_all_euks_rep.phyloprofile.valid - Feature architecture aware phylogenetic profiles of the 76 representative pPCDs across 1,354 eukaryotes7. cellulase_all_forward.domains - feature architecture comparisons of all orthologs detected in 18,565 taxa to the respective seed sequences8. cellulase_all_metazoa_rep.phyloprofile.valid - Feature architecture aware phylogenetic profiles of the 76 representative pPCDs across all animals)9. PP_data - This directory contains the ready-to-use custom taxonomy database comprising all species represented in the phylogenetic profiles.<br>INSTRUCTIONS1. download and install PhyloProfile from the Bioconductor web pages2. start PhyloProfile according to the guidelines provided in the user manual3. update the custom taxonomy database into PhyloProfile according to the guidelines provided under the following URL: https://github.com/BIONF/PhyloProfile/wiki/PhyloProfile-and-the-NCBI-taxonomy-database#update-the-taxonomy-db. Note, this has to be done only once4. upload one of the provided phyloprofiles into PhyloProfile. You can now plot the phylogenetic profile. Optionally, upload also the domains file and the fasta file for full functionality