Introduction to Bioinformatics: CMSC54610-1, Spring quarter 2006.

Some frequently asked questions about the homework for Lecture 3

• When you ask us to 'Find all sequences that have the exact six-letter sequence in it', do you want us to list each matching sequence by name?
  • No, just the `classes' of sequences. In the example I showed in class, I would say that these were all prions, and give the data for just one of them (say, the human prion). But you could also say how many different species of prions (or whatever other kind of protein) you found.
• By 'unique sequences', do you mean sequences that we are searching for which do not have an exact match? If so, I did not have any non-exact matches and I'm not sure how to approach this question.
  • No, I still mean exact match. But I just mean one representative from the family. Again, I would consider the `prion' to be just one sequence in this context.
• In summarizing the results, what are the key points that I should report on?
  • First of all, say what the different types of proteins were, e.g., 36 prion proteins from various species, one viral protease, and so forth. Do this for all the different classes of proteins that show up.

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• Database searches
  • Applying BLAST to find matches to short sequences
  • see the Search for short, nearly exact matches button on the NCBI Blast website
  • Use it to do homework (3.2) below
• Homework problems:
  • (3.1) Align the sequences for Chk1 and Pdk1
    • Download the PDB files 1IA8 (for Chk1) and 1UVR (for Pdk1) from the Protein Data Bank (PDB) in FASTA format
    • Perform a sequence comparison using ClustalW
    • How many residues are an exact match in the alignment?
    • How many gap characters are in the alignment?
  • (3.2) Each of you is to do a blast search on the following six sequnces assigned to you individually:
    • last name: sequence1, sequence2, sequence3, sequence4, sequence5, sequence6
      • Burke: EKYYKE, EKFFKD, EKFFKE, EKYYKD, DKFFKD, DKFFKE
      • Fraser: DKYYKD, DKYYKE, EKYYRE, EKFFRD, EKFFRE, EKYYRD
      • Holper: DKFFRD, DKFFRE, DKYYRD, DKYYRE, ERYYKE, ERFFKD
      • May: ERFFKE, ERYYKD, DRFFKD, DRFFKE, DRYYKD, DRYYKE
      • Pinnamaneni: ERYYRE, ERFFRD, ERFFRE, ERYYRD, DRFFRD, DRFFRE
    • Find all sequences that have the exact six-letter sequence in it
    • Find all unique sequences and characterize them based on the description of the sequence
    • Write a short report summarizing your results.