Assignments for week 1

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.
• The lectures notes for the first lecture http://www.embnet.se/embnet/sennedub
• A local server for alignments This server aligns two protein sequences with different matrixes.
• Added links during the course. If you find an interesting link please add it here.

Practical Reports

1. BLAST-SEARCHES:
• Localize 3 different BLAST servers and examine them with the test sequences found here. What blast servers did you find ?
  
  What are this sequence related to ?
  Sequence 1:
  Sequence 2:
  Sequence 3:
  
2. FASTA-SEARCHES:
• Try the same sequences with FASTA. What fasta servers did you find ?
  
  
3. Are any of these sequences related to a protein with a known structure ?
   
4. ALIGNMENTS:
• Align the two plastocyanin sequences 2pcy and 7pcy. Which one has a gap ?
  Is the same alignment obtained with all matrixes ?
  With global and local alignment ?
  With all gap-penalties ?
  
• Azurin (2aza) and plastocyanin (2pcy ) are related. Can you get them to align nicely ? With what matrix, what gap-penalties ?
  
5. INTERNET SEARCHES:
• Go to NCSA biology workbench ( http://biology.ncsa.uiuc.edu/) and run the demo. Look at the ALPHA-CHYMOTRYPSINOGEN COMPLEX WITH HUMAN PANCREATIC in rasmol. How many helixes does rasmol think this structure has ?


• Go to entrez (after finding it). Give me the address of it. And search for actin. Are there any related proteins ? Any proteins of similar structure ? What class of a protein is actin.


• Describe what BCM Search Launcher can do.


• Which of the sites with list to differents services on the internet is (a) Most up to date ? (b) easiest to understand ? (c) best ?

To understand before the reading seminars.

• Describe the difference between BLAST, FASTA and Smith & Waterman



• Describe some of the protein sequence databases available



• Describe the difference in performance between BLAST FASTA and Smith & Waterman according to Pearson. How is the performance measured ?



• How do I find something on the internet ?