Dr. Jennifer W Weller @ UNC Charlotte Outreach

This page includes links to presentations, demonstrations, tutorials, Web portals to Bioinformatics tools and pipelines, interesting articles and pictures and anything else we think it would be fun or useful to know. If you have suggestion, please send us an email providing the link and an explanation for why you like it.

(BLAST)

You can always start with Wikipedia and see how it goes: https://en.wikipedia.org/wiki/BLAST
BLASTing through the kingdom of Life http://digitalworldbiology.com/BLAST/62000sequences.html
This includes a BLAST tutorial http://v3.digitalworldbiology.com/BLAST and a BLAST lab that you can print out.
Julian Trubin hosts a site with some bioinformatics experiments, including an explanation of BLAST and some labs: http://www.juliantrubin.com/encyclopedia/bioinformatics/blast.html
Science Buddies The Tree of Life – I is basic http://www.sciencebuddies.org/science-fair-projects/project_ideas/Genom_p004.shtml
Using BLAST and ExPASy for examining avian influenza H1N1 variability http://gep.wustl.edu/curriculum/course_materials_WU/introduction_to_genomics/dna_sequencing_labs

T-coffee http://tcoffee.crg.cat/apps/tcoffee/index.html
ClustalW http://www.clustal.org/clustal2/

there is a PBS tutorial at http://www.pbs.org/wgbh/evolution/

The DNA Learning Center has a good animation library showing early DNA sequencing methods https://www.dnalc.org/resources/animations/sangerseq.html
Starting with Wikipedia, which takes you from the earlies versions through current state-of-the-art technologies: https://en.wikipedia.org/wiki/DNA_sequencing
Genome News Network has a good build-up to the technical terms: http://www.genomenewsnetwork.org/resources/whats_a_genome/Chp2_2.shtml
Extreme Tech has a shorter description and focuses on the newer technologies, without as much background linked to the topic: http://www.extremetech.com/extreme/214647-how-does-dna-sequencing-work
A pretty good description of the original ‘high-throughput’ sequencing technology, Sanger sequencing with fluorescently tagged nucleotides and some nice cartoons, is given here: http://www.biol.unt.edu/~jajohnson/DNA_sequencing_process
and another is here http://www.udel.edu/dnasequence/Site/How_does_DNA_sequencing_work.html
The Wellcome Trust has a Your Genome (YG) site that describes a number of methods and technologies, including Illumina next-generation sequencing http://www.yourgenome.org/facts/what-is-the-illumina-method-of-dna-sequencing and http://www.yourgenome.org/video/sequencing-at-speed
The YG site also explains the very newest, Thrid-generation technology, SMRT from Pacific Biosciences http://www.yourgenome.org/stories/third-generation-sequencing

DNA Barcoding 101 The formal site is at Cold Spring Harbor Laboratories, they provide wet-lab protocols and descriptions of how to use the selected gene sequences. http://www.dnabarcoding101.org/
The DNA Learning Center has an animation showing how the DNA bar coding works https://www.dnalc.org/resources/animations/dna-barcoding.html
The Barcode Blog (this is very technical, but shows where this expertise can lead you). http://phe.rockefeller.edu/barcode/blog/
The international Barcode of Life community has a Web site with some nicely presented basic information: http://www.ibol.org/about-us/what-is-dna-barcoding/
Our friends at Wikipedia chime in: https://en.wikipedia.org/wiki/DNA_barcoding

The YG site has a non-technical description http://www.yourgenome.org/facts/how-do-you-put-a-genome-back-together-after-sequencing
Also from Genome News Network http://www.genomenewsnetwork.org/resources/whats_a_genome/Chp2_3.shtml#chp2#8
If you want a Lab that does NOT use computers but shows the pronciples of DNA Assembly, there is one here: http://www.nslc.wustl.edu/elgin/genomics/gsc/AssemblingSeq.pdf

Bill Pearson (created the FASTA algorithm) has written a chapter that explains the theory and the practice of doing homology searches. http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3820096/
This article from Science in School has a good explanation of the idea behind calculating distances between sequences (and does not assume you have a computer). http://www.scienceinschool.org/2010/issue17/bioinformatics

A great set of labs, with good explanations is provided by the Cyberinfrastructure for Phylogenetic Research collaboratory through their outreach section : http://www.phylo.org/sub_sections/outreach/outreach_c
The Howard Hughes Medical Institute has a large number of modules – one of these is Creating Phylogenetic Trees from DNA Sequences. http://www.hhmi.org/biointeractive/creating-phylogenetic-trees-dna-sequences
A good starting point that gives short descriptions of different concepts with more detailed descriptions (and links to some nice videos as well) if you want to dig deeper is here: http://www.indiana.edu/~ensiweb/phylo.%20tree.html

The original quality score was devised by Phil Green for ABI Sanger-fluoresccent dye sequencers, called Phred Scores, described here in Wikipedia with some nice examples https://en.wikipedia.org/wiki/Phred_quality_score
From Illumina, some of the ideas are shown here http://www.yourgenome.org/facts/what-happens-to-dna-sequence-when-it-comes-off-a-sequencing-machine
Sandra Porter posted an explanation of quality score origins and use on her Descovering Biology in a Digital World blog: http://scienceblogs.com/digitalbio/2006/07/10/dna-sequence-quality-part-i-qu/

The DNA Subway analysis pipelines are sponsored by the iPlant Collaborative (now CyVerse) http://dnasubway.iplantcollaborative.org/

Integrated lectures and Labs can be found at the Northwest Assocation for Biomedical Research https://www.nwabr.org/teacher-center/advanced-bioinformatics-genetic-research#overview
The Biology Student Workbench has become the molecular Science Network, a lot of labs/tutorials to show how to carry out bioinformatics research: http://bioquest.org/bioinformatics/module/ (older) and http://medsocnet.ncsa.illinois.edu/MSSW/ (current).

A somewhat simple reminder (but nice pictures) at the cK-12 site : http://www.ck12.org/biology/Chloroplasts/lesson/user:bXJmb3gyMThAZ21haWwuY29t/Photosynthesis:-Chloroplasts/
Science buddies includes a chloroplast sequencing module, similar to what we are proposing for the summer: http://www.sciencebuddies.org/science-fair-projects/project_ideas/Genom_p012.shtml#background

Starting with Wikipedia: https://en.wikipedia.org/wiki/RuBisCO
A nice description at the ProteinDataBank: http://pdb101.rcsb.org/motm/11

Starting with Wikipedia: https://en.wikipedia.org/wiki/16S_ribosomal_RNA
There is a whole database of rRNA sequences (European), called SILVA: http://www.arb-silva.de/
And another one (US) called the Ribosomal DataBase, or RDP, here: https://rdp.cme.msu.edu/

Gene Annotation: under construction
PCR: under construction
PCR primer design: under construction

Topic:
Chestnuts and Chestnut Blight - there are a number of University and USDA research labs that conduct and/or fund research on the American Cehstnut (and its relatives) and the two main diseases that have affected them.

The American Chestnut Foundation is a group of citizens who have helped raise money to fund projects, and breed resistant hybrids, allowing citizen-scientists to participate. Last year Steve Barilowitz, treasurer of the local chapter, participated in the class. The ACF Web site
Although maybe a little too data-centric, this is a site where whole groups of researchers deposit data to share with each other and the public. THe Fagaceae are chestnuts, beeches and oaks. Fagaceae Genomics Web
The US Department of Agriculture -Natural Resources Conservation Service has Web pages that profile plants - here is the page that talks about the American Chestnut, showing images of leaves and trees, and a map of where they occurred historically and now: PLANTS - chestnut

Topic:
The polymerase chain reaction - Background
Animating how PCR works is a favorite video and animation theme

The PCR Song from researchers at BioRad was a hit a few years ago Link
An animated and narrated description of PCR Link
You do have to know how DNA is copied (replicated) before PCR can happen, so here is a description of that process Link

Topic:
Science Blogs - a number of scientists have shown real talent for writing about their interests for non-experts, and a number of journalists have taken on the task of making science accessible and exciting. I have providing links to a few of my favorite science blogs here, I hope you find one or two that you want to follow.

Sandra Porters blog, Discovering Biology in a Digital World is partly interesting to me because she has done a lot to make sequencing and bioinformatics accessible to high school and community college students DigitalBio
PZ Meyers is a developmental biologist who is interested in evolutionary questions - and is very entertaining Pharyngula
Jonathon Eisen is a professor at UC Davis who does lots of sequencing ( a 'genomicist') and analyzes the results (a 'bioinformatician) and writes well about the implications of the science he does The Tree of Life