Databases and Software

NCBI— A suite of interlinked bioinformatics databases that detail DNA, protein, gene and disease data.

OMIM—Online Mendelian Inheritance and Man. An extensive medical database of human disease phenotypes and associated genes.
MapViewer—Used to visualize genetic, physical, gene and other maps.
BLAST—Basic Local Alignment Search Tool aligns a protein or nucleotide (DNA) sequence against the billions in the database to look for matches.  Can be used to find difference between sequences, or to look for similarity between known sequences.
PubMed—Collection of millions of biomedical papers that include many free, full text articles.

BLAT—from UC Santa Cruz aligns a nucleotide sequence against only human reference sequences.  Can be used to to find difference between sequences, or to look for similarity between known sequences.
GENOME BROWSER—from UC Santa Cruz. A genome position can be specified by the accession number of a sequenced genomic clone, a chromosomal coordinate range, or keywords from the GenBank description of an mRNA.
STRING—Shows gene/protein interactions and associations
STITCH—Shows gene and drug interactions
KEGG—Used as a reference knowledge base for biological interpretation of large-scale datasets generated by sequencing and other high-throughput experimental technologies
Sequence Analysis Programs—University of Michigan provides and up-to-date list of programs (many free) that you can use to analyze DNA sequence.  Several are below:

Sequence Scanner Software 1.0— free PC-based program from Applied Biosystems inc.
Trace Viewer—CodonCode Aligner—A free demo version of a program for sequence analysis on both Windows and Mac OS X.  Note that it is free for academic users.
FourPeaks—Mac OSX free software that allows you to work with sequence data

SymAtlas—A free gene portal system where you can learn about gene and protein function
Primer 3—Used to design primers for an area of interest

Virtual Labs and Other Teaching Resources

Dolan DNA Learning Center—Great site for labs, activities, new information and much more!

Genetic Origins—Check out the sequencing service where they will sequence your class for FREE!!!
Sequence Server

PCR animation—Excellent animation of the PCR process from the website that Kary Mullis who won a Nobel prize for PCR in 1993.
PCR song—Humorous, high quality production video about PCR from BioRad (a lab supply company).
Partnership for Biotechnology and Genomics Education - PBGE has some useful virtual labs available.
HHMI BioInteractive -

HHMI - Genomics and Chemical Genetics - A short overview of bioinformatics.  You can order the holiday lecture series on DVD.  Explore the website for even more resources.
HHMI - Leading-Edge Bioinformatics - Short videos about bioinformatics from the 2010 holiday lecture series.

Lesson Plans, Modules, and Activities

Issues in Genomics from Action Bioscience - ActionBioscience has some articles on the applications and ethics of genomics.
Bioinformatics Lessons on ENSI web - Molecular Evolution Lessons
Molecular Science Student Workbench - Scroll through the lessons to find some more bioinformatics activities for high school.
Biolink Biotech Teaching Materials - A long list of resources and lessons for teaching biotechnology and bioinformatics concepts.
Two Bioinformatics Lessons from Montgomery Blair High School - Two medical related activities are available, one on phenylketonuria and the other on amyloidosis.
Bioinformatics in High School - An introductory power point for teachers and students.
Bioinformatics & Research Computing - A collection of lecture notes, homework problems and student labs from the BRC / Whitehead workshops.


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