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Bielefeld University Center of Biotechnoloy Institute of Bioinformatics BiBiServ
 
Pairwise Alignments - Exercise 1
Browse to Dotlet to analyze the following sequences with Dotlet:
  1. Plot the D. melanogaster SLIT protein (accession: P24014) against itself. Select zoom level 1:5 in the rightmost combobox to get an overview of the whole dotplot. How many domains does this potein have and how often is each repeated? You can use the UniProt- or Pfam- database to find more information about the domains. How does the structure of the protein look like?
  2. Plot the B. subtilis UTP-glucose-1-phosphate uridylyltransferase gene (accession: L12272) against itself. The sequence has a translation terminator, which in this case is a stem-loop in the RNA molecule. How can you recognize this in the dot plot? What does the dot plot pattern mean with regard to the sequence?