Introduction to Bioinformatics: CMSC54610-1, Spring quarter 2006.
Lecture 3
Database searches
Dehydrons as markers to discriminate similar proteins
(PDF slides used in the lecture are here)
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.
- Homework is due by the beginning of the next class.
- Preferred: Homework should be turned in physically before the start of the class
- Emergency: send it to me electronically in standard formats.
Term paper:
outline due due 6th week