This repository includes the notebooks and data from a preliminary systematic analysis of viral TPs, conducted as part of Juan Carlos Ramírez Montáns' Master's Thesis, supervised by Modesto Redrejo Rodríguez (Department of Biochemistry, @UAM).
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- Main workflow notebooks and scripts
File Description 01_Predataset_Clustering.ipynb Predataset FASTA sequence retrieval and dual clustering (BLAST2seq+K-Means+PCA, CD-Hit). Open it in Google Colab. 02_Surface_Charge_Density_Distribution.ipynb Surface charge density distribution asymmetry computation, assessment and scrutiny. Open it in Google Colab. 03_Secondary_Structure.ipynb Secondary structure composition calculation and assessment of its TP-discriminant potential. Open it in Google Colab. 04_DNABIND_ConfusionMatrix.ipynb DNABIND DNA-binding classifier evaluation for TP discrimination. Open it in Google Colab. 05_FoldSeek.ipynb Structure-based PSI-BLAST (via RESTful API access) homology search, results processing (sieving, prefiltering, sorting and deduplication) and taxonomic information retrieval. Open it in Google Colab. 06_PSI_BLAST.ipynb Sequence based PSI-BLAST homology search, results processing (sieving, prefiltering, sorting and deduplication) and taxonomic information retrieval. Open it in Google Colab. 07_taxonomizr_Taxonomic_Inspection.ipynb taxonomizr-based taxonomic scrutiny of candidate homologs' lineages. Open it in Google Colab. 08_qTMcluster_processing.ipynb qTMcluster (structure-based clustering of Foldseek-yielded candidate hits) data processing and evaluation of query coverage impact on qTMcluster co-clustering performance. Open it in Google Colab. 09_Results_Clustering.ipynb Compound Foldseek and PSI-BLAST results merger and deduplication, FASTA sequences retrieval and sequence-based CD-Hit clustering. Open it in Google Colab. 10_Contig_retrieval_inspection.ipynb Genome/contig retrieval of IPG-yielded representative proteins. Open it in Google Colab. 11_Genome_Proteome_Annotation.ipynb Retrieval of GBK-format representative proteomes, FASTA format conversion, PHROG execution and results scrutiny, geNomad execution and scrutiny, PHROG-geNomad cross-reference and virus-free contig shortlisting. Open it in Google Colab. 12_Roll_back.ipynb Merger of sequential results dataframes into final results whole-width dataset (FULL_results+GenomeID+Tax+Cluster+BLASTp_Synonyms+IPG+Non-Viral+eggNOG+Pol+COG.csv). Open it in Google Colab. 13_Plots_and_Statistics.ipynb R scripting for plotting. Open it in Google Colab. PSI-BLAST.sh Sequence based PSI-BLAST homology search BLASTp.sh Sequence based BLASTp homology search for GenBank homologs def_geNomad4TP_multiFASTA.py Python script for running geNomad on multi-FASTA file PHROG4TP_new.py Necessary Python scripts for running PHROG PHROG4TP_hmmbuild.py Necessary Python scripts for running PHROG - Results files
File Description TP_Predataset.csv Predataset parseable dataframe TP_Predataset_updated_2025_05.pdf Updated (2025/05) Predataset with full-length taxonomic breakdown TP_Clustered.clstr_n4c06g1.clstr Predataset CD-Hit clustering results TP_Dataset.csv Initial TP dataset (clustered predataset) TP_Dataset.zip Compressed file containing initial TP dataset's AlphaFold2-yielded predicted structural models (PDB) FULL_results+GenomeID+Tax+Cluster+BLASTp_Synonyms+IPG+Non-Viral+eggNOG+Pol+COG.csv Main final dataframe encompassing results across all processing and scrutiny steps FINAL_results_updated.csv Raw curated results dataset merging Foldseek- and PSI-BLAST-yielded candidates Dedup_FoldSeek_results_low_updated.csv Curated (sieved, prefiltered, sorted and deduplicated) Foldseek-yielded candidate structure-based homologs' dataset Species_PSI-BLAST_results_updated.csv Curated (sieved, prefiltered, sorted and deduplicated) PSI-BLAST-yielded candidate sequence-based homologs' dataset
- András Szilágyi DNABIND classifier (https://dnabind.szialab.org/)
- Foldseek RESTful API (https://search.foldseek.com/api/)
- FoldMason (https://search.foldseek.com/foldmason)
- ClustalΩ (https://www.ebi.ac.uk/jdispatcher/msa/clustalo)
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