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MICa 8006
Protein Sequence Analysis

Homework 6

Due before class, Tuesday, October 17, 2006

Part A (15 pts) Protein Analysis

In this part, you will use test5.pep, which is on the class website in fasta format. Previously, you have used genomic sequences: full-length, very accurate, either directly sequenced or translated from genomic DNA. The protein sequences in test5.pep are derived from Expressed Sequence Tag (EST) data: possibly truncated at either end, 1-2% error rates, more *=X=unknown residues. These are vertebrate, eukaryotic sequences, part of an ongoing UM research project, and similar to the sequences you will analyze for your term project.

This exercise is meant to help you decide on a personal strategy to use to analyze a set of unknown protein sequences. Analyze each sequence using the Web, GCG, BioPerl and/or your own programs. Use several modules, websites, and/or programs, as many as is appropriate, in a reasonable order, for each sequence. You are not required to use the same software on each sequence. Read Part B before starting this part of the homework. Write a report on these sequences, as you did in HW5A, for a person who is not familiar with protein sequence analysis. Include what analyses you did, in what order.

Submit: a short report on all you learned about each of these proteins, with output that supports that report. Don't include negative output, instead state in the report that you ran the test and the results were negative. Describe what each test (with positive or negative results) measures, in terms understandable by a person who is not familiar with protein sequence analysis.

Part B (15 pts) Perl - program control

As part of the analysis in Part A, demonstrate the use of Perl to control GCG, by using it to run two or more GCG protein sequence analysis modules on one or more sequences in test5.pep.

Submit: a printed copy of your program and the output it produces when it is run. Also, email your program to Flora Fan at fanx0038@umn.edu

February 21, 2008 Lynda Ellis 

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