This page provides links to files you will need for some of the labs.

Day 1 Files
Assessment Forms

• Pre-assessment link
• Daily Assessment link
• Final Assessment Link

Working Files

• Watson Speech, Complete text Link
• Watson Speech, with spaces removed Link
• Frequency Data Link
• Encoding/Decoding ASCII Link
• DNA Subway set-up notes Link

Presentations

• Weller: Encoding and transforming files Link
• Weller: Ways to compare and visualize DNA Sequence (DNA Subway Blue Line) Link

Additional Explanations

• From the NWABR, a lesson on comparing DNA sequences: identifying nucleotide changes and then using a tree format to visualize the differences Link
• From the NWABR, more details on setting up a table including the frequency of sequence differences for the set you are comparing Link
• From the NWABR, more details on how DNA sequence data is produced and quality is determined Link

Day 2 Files

Presentations

• Dahlia Shvets Introduction to Using R for graphing Data Link
• Weller: Sample selection and using genomics resources Link
• Weller: Sequencing Tecnologies Link
• Weller: Sequence Data QC and Assembly Link
• Smith: Determining Sequence Relatinships Link
• Smith: Gene Annotation with GeneBoy Link

Data Files

• The gel images for Sequence interpretation Link
• The instructions for sample and genomic information finding Link
• Sequences for QC and Assembly Lab Link
• C mollissima Full CP genome sequence Link
• C. mollissima Full rbcL DNA sequence Link
• C collissima DNA Bar Code rbcL sequence Link
• Cacao Chloroplast DNA sequence HQ336404 Link
• C. Prunus persica Chloroplast DNA sequence HQ336405 Link
• Castenea millissima Rubisco HQ336406 Link
• Selected sequences in FASTA 69214 Link

Additional Explanations

• Overview of the lab on DNA barcode for land plants Link
• Overview of the lab on gene annotation Link

Day 3 Files

Presentations

• Weller: PCR and PCR Primer Design Link

Labs

• Directions to follow along with the lecture Link
• Student Lab - design primers for C mollissima rbcL bar code region Link
Tutorials (step-by-step primer design)
• PCR primer design - explanation about the factors like temperature and length Link
• PCR primer design - an example using the 16S rRNA gene in bacteria Link