Primer Design exercise and solution for three Canis species:
http://universitygenetics-technology.blogspot.com/2013/02/primer-design-exercise.html
Thoughtful video on principles of primer design with useful sketches: https://www.youtube.com/watch?v=tUyBwiyMsSU
BARCODE SEQUENCE IDENTIFICATION and ALIGNMENT TOOLS
NCBI nucleotide Blast: https://blast.ncbi.nlm.nih.gov/Blast.cgi?PROGRAM=blastn&PAGE_TYPE=BlastSearch&LINK_LOC=blasthome
BOLD barcode identification database: http:/v4.boldsystems.org/
Online Sequence Alignment Tool – enter sequences and get them to slide into alignment for base comparison: https://www.ebi.ac.uk/jdispatcher/msa/clustalo
Sequence Trace Chromatogram viewer for *.ab1 files: https://www.gear-genomics.com/teal/
PRIMER DESIGN AND ANALYSIS TOOLS
Overview of primer design and pitfalls: http://bioweb.uwlax.edu/GenWeb/Molecular/Seq_Anal/Primer_Design/primer_design.htm#programs
Eurofins oligo analysis tool: (Tm and dimers) – https://www.eurofinsgenomics.eu/en/ecom/tools/oligo-analysis.aspx
Fisher Primer Annealing Temp calculator:
https://www.thermofisher.com/us/en/home/brands/thermo-scientific/molecular-biology/molecular-biology-learning-center/molecular-biology-resource-library/thermo-scientific-web-tools/tm-calculator.html
Sigma-Aldrich free analyzer with hairpin (secondary structure) and dimer assessment http://www.oligoevaluator.com/OligoCalcServlet