Assignments for week 3

Internet and Searching databases.

Usefull Links For This Week

• BCM-sequence launcher A start page to submit BLAST, FASTA and other searches. Very usefull!
• The course 96 list of links. This is the set of links that was found before the course.
• Added links during the course. If you find an interesting link please add it here.
• Cinema A multiple sequence alignment editor
• Hidden Markov Model at UCSC
• NCSA Workbench
• MaxHom Multiple sequence alignment
• A good Prosite PATTERN site
• A good Prosite MATRIX site
• Neural Net to predict cleavage sites

Practical Reports

1. Motifs & Signals
• Find the possible cleavage sites in these peptides. How many (if any) cleavage sites did you find ?


• Perform a prosite PATTERN search for the protein IQGA_HUMAN in SWISSPROT Did you find anything ? What in that case ?


• Perform a prosite MATRIX search for the protein IQGA_HUMAN in SWISSPROT Did you find anything ? What in that case ?


2. MULTIPLE-SEQUENCE ALIGNMENTS:
• Use the sequences. used in the assignments of the first week and try to do a multiple sequence alignment with these sequences and the related sequences you find in the database. NCSA might be a good place to do this. Another good tool might be Cinema



3. THREADING
• Use the one of the threadig sequences. found in the data directory and try some threading/HMM methods. To see if you find some possible related structure to this fold.

To understand before the reading seminars.

• Describe the advanteges with multiple sequence alignments


• Describe the different terms that have been used in different "threading" programs


• What is the froozen approximation ? Why is it a problem ? What have people done to try to overcome it ?



• What are the "new" threading methods.



• What is a Hidden Markov Model ?



• What can be understood by signal sequence analyzis.



• Descibe some important aspects to think about when refining a Neural Net ?