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Table 1 Tools, databases and tutorials relevant for the identification and characterization of the host-pathogen share-ome. All URLs were accessible as of January 2021

From: A systematic bioinformatics approach for large-scale identification and characterization of host-pathogen shared sequences

Database, Tool, and Tutorial URL
NCBI Entrez Databases http://www.ncbi.nlm.nih.gov
NCBI Entrez Protein Database http://www.ncbi.nlm.nih.gov/protein
NCBI Entrez Taxonomy Database http://www.ncbi.nlm.nih.gov/taxonomy
STRING Viruses database http://viruses.string-db.org/; version 11.0
CD-HIT http://weizhongli-lab.org/cd-hit/
E-Utilities esearch-efetch https://www.ncbi.nlm.nih.gov/books/NBK25500/#chapter1.Demonstration_Programs
entrezEsearch https://github.com/gwatiyapJ/SiMiLyG
kmerslicer https://github.com/gwatiyapJ/SiMiLyG
Unipro UGENE tools http://ugene.net/
UniProt Retrieving and ID Mapping tool https://www.uniprot.org/uploadlists/
CateGorizer https://www.animalgenome.org/tools/catego/
Unix utilities https://unix.stackexchange.com/
Tutorial 1: Notes on how to use R for doing statistical analysis and graphics https://cran.r-project.org/manuals.html
Tutorial 2: Unipro UGENE Manual Version 37, 2020. Consists of user guide to bioinformatics tools for alignments, genome sequencing, data analysis, and amino acids sequence visualization, among others. http://ugene.net/downloads/UniproUGENE_UserManual.pdf
Tutorial 3: User’s guides on implementation for removing duplicates sequences and generating representative sequences http://www.bioinformatics.org/cd-hit/cd-hit-user-guide.pdf
Tutorial 4: Webinar: Introduction to NCBI’s E-utilities API https://www.youtube.com/watch?v=iCFVVexp30o&t=2561s