Exercises
·Unix Introduction
·BLAST
·PERL
·Genbank
·BLAST, GCG
·GCG
·Seqlab
·Synthesis
·MSA
·Paup
·Phylogeny
·Examine


·An editor primer
·A GCG cheatsheet
·Flat2fasta homework
·Dynamic Programming homework
·High scoring words homework
·GCG homework
·Seqlab homework
·Mystery sequence homework
·Paup homework

A first pass using GCG


Given the following sequence fragment:
krsranmnnstttgpanntssnktfldnfeetrtnkllde
do the following:
  1. Discover what sequence in the public databases is most similar to it.
  2. Download this sequence to your account
  3. Using this starting point, find sequence in the public databases which may be homologous to it for the following model organisms: Saccharomyces cerevisiae, Caenorhabditis elegans, Arabidopsis thaliana, Mus musculus, Homo sapiens
  4. Report on the quantity of identity between the initial search transcript and that found in these organisms. Do so in a table with columns for: organism, accession/id #, number of identities, number of similarities, # gaps, and any available statistical information.
  5. Using gcg, perform a dotplot between a) the human and yeast versions and b) the mouse and human versions of the protein. (I suggest setting your plotter to a png or gif output and inserting the output into your document).
  6. Examine the plot to look for insertions/deletions, tandem repeats, inversions, or other interesting features and report them.