Csc334 DT lab Ideas

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• Get familiar with Proce55ing Lab #0
• Get a DNA sequence Lab #1
• Get a protein sequence Lab #2
• given a series of nucleotides, find and display the 6 reading frames
• finding repeats within a sequence
• BLAST lab: take a sequence (protein and/or DNA) and find other sequences that are close to it
• given N sequences that overlap, find the best way in which they form a long sequence. Use processing and a circle approach to represent them
• display alignment of two sequences Lab #3
  • limit to end to end overlapping
  • from output of blast
  • from result of computing local alignment

• Orfing: (page 146) Finding a sequence longer than some number (proteins are typically 350 residues in length, and at least 100 minimum), between a start (ATG), and a stop (TAA, TAG, TGA) sequence.

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FoldIt! http://fold.it. Read NYT Article If You Have a Problem, Use Innocentive to Ask Everyone for background.

• Could do a few labs from the NCBI 12 mini-course Web page. (www.ncbi.nlm.nih.gov/Class/minicourses)

I tried a few... they are fairly cryptic and require good knowledge of biological terms...

• • Bioinformatics Quick Start
  • Making Sense of DNA and Protein Sequences
  • Unmasking Genes in Human DNA
  • Identification of Disease Genes
  • Correlating Disease Genes and Phenoypes
  • BLAST Quick Start
  • EntrezGene Quick Start
  • Structure Analysis Quick Start
  • MapViewer Quick Start
  • GenBank Quick Start
  • Entrez Quick Start
  • Microbial Genomes Quick Start

• Lab on Sequence Logo with Processing. Good reference can be found here.

Image taken from http://www.clcbio.com/index.php?id=869

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