Difference between revisions of "Csc334 DT lab Ideas"

Revision as of 16:31, 31 July 2008

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.

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...

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 FoldIt!  [http://fold.it/portal/adobe_main http://fold.it].  Read NYT Article
 [http://www.nytimes.com/2008/07/22/science/22inno.html?pagewanted=all 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. ([http://www.ncbi.nlm.nih.gov/Class/minicourses/ 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
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