Bionformatics Resources

General Bioinformatics Resources

Depending on your project, you may find some of the following resources useful - please note that this is by no means an exhaustive list, just a starting point for your work - there are many more helpful resources out there. Feel free to discuss with Dr. Feeney if you have any questions.

• How to Access Data from Public Databases

• Links to some key public databases.

• Get Started with GitHub documentation

• Galaxy Video Lectures

Useful tools/websites

• Interactive Tree of Life (iTOL): Useful for visualising phylogenetic trees, and editing their presentation

• ExPASy resource portal: A suite of different bioinformatic resources

• JalView: multiple sequence alignment editing, visualisation and analysis

• PyMol: 3D molecular visualisation

Streptomyces/actinomycetes resources

• StrepDB

• Tables of Streptomyces coelicolor reciprocal BLASTP hits

• antiSMASH

• ActinoBase

Phage project resources

• Actinobacteriophage Database

• Phage tutorial 1: In this first tutorial, we go through how to create and name a new history in Galaxy, identify and import phage genome sequences into Galaxy, and annotate and examine the imported phage genomes

• Phage tutorial 2: In this tutorial, we work through how to create a phylogenetic tree for a gene/protein of interest

• Phage tutorial 3: in this tutorial, we go through some of the possible downstream analyses that can be done once you have identified gene(s) or protein(s) of interest in your phage genome, including: BLAST analysis, structural prediction/analysis, analysis of physicochemical properties, and codon usage calculations

• Phage tutorial 4: This tutorial looks at different ways of analysing the host genomes, including BLAST analysis, searching for CRISPR-Cas systems and other antiphage defenses, and analysis of secondary (specialised) metabolite production

actDES resources

• Schniete, J. K., Selem-Mojica, N., Birke, A. S., Cruz-Morales, P., Hunter, I. S., Barona-Gomez, F., & Hoskisson, P. A. (2021). ActDES - a curated Actinobacterial Database for Evolutionary Studies. Microbial genomics, 7(1), mgen000498. https://doi.org/10.1099/mgen.0.000498

• e-seminar explaining actDES

• actDES GitHub repository

• actDES FigShare page

• actDES Python script and YouTube walkthrough

Additional selected tutorials

Some workshops going through some bioinformatics topics, which you may find helpful to work through to review basic concepts:

• BM214 workshop 2: sequence searching

• BM211 workshop 5: phylogenetic trees

• BM329 workshop 1: microbial identification

• BM425 workshop 1: genome analysis