There are a number of great tutorials on the web for bioinformatics-related applications and topics. Here are a few that I’ve run across. Are there any missing? Feel free to add any that I might have left out in the ‘comments’ section!
- UCSC Genome Browser
BIT 1.1: UCSC Genome Browser: Getting DNA Sequence (3:57)
BIT 1.2: UCSC Genome Browser: Using Annotation Tracks (5:47)
BIT 1.3: UCSC Genome Browser: Locating Intron-Exon Boundaries (4:56)
BIT 1.4: UCSC Genome Browser: Searching with BLAT (6:14)
- NCBI BLAST
BIT 2.1: BLAST Link (7:24)
BIT 2.2: Do I Need BLAST? The Use of the Related Sequences Tool (6:53)
BIT 2.3: Nucleotide BLAST (5:46)
BIT 2.4: Nucleotide BLAST: Algorithm Comparison (6:14)
- Other NCBI Resources
BIT 3.1: OMIM and OMIA (6:34)
BIT 3.2: Entrez Gene (5:35)
Research Tips: Molecular & Cellular Biology from Health Sciences Library, Anschutz Medical Campus, University of Colorado Denver
- UCSC Genome Browser sponsored by the University of California Santa Cruz Bioinformatics Group
- Galaxy Analysis Tool sponsored by the Galaxy team at Pennsylvania State University
- VISTA Comparative Genomics Tools sponsored by Lawrence Berkeley National Laboratory
- Genome Variation Server (GVS) sponsored by the National Heart, Lung, and Blood Institute (NHLBI) and the University of Washington
- SeattleSNPs sponsored by the National Heart, Lung, and Blood Institute (NHLBI) and the University of Washington
Additionally, Model Organisms are a key tool for biomedical research, leading to breakthroughs in all fields of biology. Through funding from the NHGRI and other sources, OpenHelix is currently offering seven free tutorial suites on Model Organism Databases and Tools.
- GBrowse, an open source software tool for developing genome browsers.
- RGD, Rat Genome Database
- MGI, Mouse Genomics Informatics
- WormBase, a C. elegans genome database
- ZFIN, Zebrafish Information Network
- FlyBase, a database of Drosophila genes and genomes
- SGD, Saccharomyces Genome Database
National Library of Medicine
- PubMed Tutorial, including information about MyNCBI.
- NIH Grant Tutorials
- Specialized Information Services (SIS) Division website
- Biomedical Research and Informatics page
- Human Genome page
- NLM Fact Sheets
- Medline Plus Interactive Health Tutorials
- Genome Workbench Tutorials
- Cn3D 4.1 Tutorial
- BLAST information guide
- Entrez tutorial
- PubMed Tutorial
- Entrez GEO Profiles and Entrez GEO DataSets query tutorial
- PubMed Central
Other helpful resources from NCBI:
- NAWBIS course (click on “modules”) http://www.ncbi.nlm.nih.gov/Class/NAWBIS/index.html
- Introduction to Molecular Biology Resources course (click on “modules”) http://www.ncbi.nlm.nih.gov/Class/MLACourse/index.html
- NCBI Education site http://www.ncbi.nlm.nih.gov/Education/Science Primer
- PubChem homepage [PubChem help document]
- PubChem Compound: Search unique chemical structures using names, synonyms or keywords. Links to available biological property information are provided for each compound.
- PubChem Substance: Search deposited chemical substance records using names, synonyms or keywords. Links to biological property information and depositor web sites are provided.
- PubChem BioAssay: Search bioassay records using terms from the bioassay description, for example “cancer cell line“. Links to active compounds and bioassay results are provided.
- Structure Search: Search PubChem’s Compound database using a chemical structure as the query. Structures may be sketched or specified by SMILES, MOL files, or other formats.
- 9 BLAST QuickStart: Example-Driven Web-Based BLAST Tutorial David Wheeler and Medha Bhagwat
- 10 PSI-BLAST Tutorial Medha Bhagwat and L. Aravind
- 24 Identification of Disease Genes: Example-Driven Web-Based Tutorial Medha Bhagwat
Basic Concepts in Science: A List (entry by John Wilkins of Evolving Thoughts blog) http://scienceblogs.com/evolvingthoughts/2008/06/basic_concepts_in_science_a_li.php
- Nucleotide Analysis
Topics include: check for vector contamination, BLAST similarity search, FASTA similarity search, whole genome search, pairwise alignment, ClustalW2 multiple sequence alignment and translation of DNA/RNA into protein.
- Protein and Proteomic Analysis
Topics include: BLAST similarity search, FASTA similarity search, whole genome search, MPsrch sequence comparison, ScanPS sequence comparison, pairwise alignment, ClustalW2 multiple sequence alignment and a proteomics example.
- Protein Function
Topics include: motif searching using InterProScan, FingerPRINTScan and PPSearch.
- Protein Structure
Topics include: introduction to nucleotide structures, introduction to protein structures and bioinformatics for protein structure prediction.
- Genome Browsing
Topics include: information on the two main genome browsers available Ensembl in the UK and UCSC Genome Bioinformatics in the USA.
- Database Browsing
Topics include: summary of the interfaces available for searching mulitple databases and also a detailed explanation of the Sequence Retrieval System (SRS) provided by the EBI.
- EBI Web Services
Topics include: What are SOAP Web Services, where to get these from; how to use them and how to develop applications with these.
Online workshops in bioinformatics tools from Nicola Gaedeke at Max Planck. http://www.biochem.mpg.de/iv/work_bio.html
- Introductory Workshops
- Basic Tools
- Hands-on Training
- Comparative Genomics in Prokaryotes: