Bioinformatics Resources
Welcome to a resources page for Bioinformatics research. Here you will find a list of links for data, tools, tutorials and related resources that may be very helpful to your work.
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Software
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Python Programming Resources
- Play with code from W3’s super Python Tutorial
- Write code locally using Jupyter Interactive Python.
- Think Python, a textbook, by Allen B. Downey. Publisher Website
- The Python Programming Language
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Online
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Articles
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Tools
- Virus Explorer
- TCoffee: http://tcoffee.crg.cat/apps/tcoffee/tutorial.html
- Hidden Markov Models (Youtube): https://www.youtube.com/watch?v=TPRoLreU9lA
- The Double Helix (Documentary about DNA discovery, 17 mins): https://media.hhmi.org/biointeractive/films/Double_Helix.html
- The Chemical Structure of DNA: https://www.biointeractive.org/classroom-resources/chemical-structure-dna
- The Structure of DNA: https://www.youtube.com/watch?v=o_-6JXLYS-k
- The definition to 5' end and 3' end of a DNA strand - Simple animated HD: https://www.youtube.com/watch?v=qWZYpHSXvJo
- What happens when your DNA is damaged?: https://www.youtube.com/watch?v=vP8-5Bhd2ag
- Mutations and Natural Selection: https://www.youtube.com/watch?v=BBI7GoIyoog
- Protein synthesis animation: https://www.youtube.com/watch?v=NDIJexTT9j0
- The Lung Endothelial Cell Atlas http://www.lungendothelialcellatlas.com
- The COPD Cell Atlas http://www.copdcellatlas.com
- The COVID Cell Atlas: http://www.covidcellatlas.com
- Idiopathic Pulmonary Fibrosis Cell Atlas: http://www.ipfcellatlas.com/
- Codon Usage Database: https://www.kazusa.or.jp/codon/
- The Comprehensive Antibiotic Resistance Database: https://card.mcmaster.ca/
- ermB anti resistance gene: https://card.mcmaster.ca/ontology/36514]
- SIM: Alignment tool for protein sequences: https://web.expasy.org/sim/
- Blast analysis: https://card.mcmaster.ca/analyze
- Diamond; a Blast alternative: http://www.diamondsearch.org/index.php
- HMMER: biosequence analysis using profile hidden Markov models: http://hmmer.org/
- Gene Ontology Resource: http://geneontology.org/
- Panther Classification System: http://www.pantherdb.org/
- Blast: https://blast.ncbi.nlm.nih.gov/Blast.cgi
- EGassembler: https://www.genome.jp/tools/egassembler/
- ELM tool kit: http://elm.eu.org/
- Protein Data Bank: http://www.rcsb.org/
- Predict protein: https://open.predictprotein.org/
- String: a protein database: https://string-db.org/
- Database of protein domains, families and functional sites: https://prosite.expasy.org/
- Needleman-Wunsch algorithm Interactive demo: http://experiments.mostafa.io/public/needleman-wunsch/
- UGENE is free open-source cross-platform bioinformatics software: http://ugene.net/
- The Cell Map: http://thecellmap.org/?q=pex6
- The String Database For Analysis: http://string-db.org/
- AmiGo: Gene products and gene annotations: http://amigo.geneontology.org/amigo/landing
- Genetics Home Reference: https://ghr.nlm.nih.gov/
- Northeast Structural Genomics Consortium: http://nesg.org/galleries.html
- ModEval: An evaluation tool for protein structure models: https://modbase.compbio.ucsf.edu/modeval/
- PyMol – A user-sponcored molecular visualization system on an open-source foundation, maintained and distributed by Schrodinger: https://pymol.org/2/
- Qiime2 – is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed: https://qiime2.org/
- DrugBank – a pharmaceutical knowledge base that is enabling major advances across the data-driven medicine industry: https://go.drugbank.com/
- Augustus [gene prediction] – a software to predict genes in eukaryotic genomic sequences: http://bioinf.uni-greifswald.de/augustus/
Research Organizations
- Cataracts and Genetics: https://knowyourdna.com/cataracts-and-genetics/
- National Human Genome Research Institute: https://www.genome.gov/
- Max Planck Institute For Molecular Genetics: https://www.molgen.mpg.de/2168/en
Note
If you find a good link for Bioinformatics research that you believe would fit nicely here, please let me know!