Csc334 DT lab Ideas
- 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.
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
