BINF630/BIOL580 Fall 2009. Homework 1. Due November 5, 2009.

 

The report should be submitted by email as a Word or PDF file with the
filename "b630_f09_hw1_Your_Name.doc or .pdf". The string "b630_f09_hw1"
should be also included in the message subject line.

  1. Write a regular expression that describes the alignment in the box.
  2. Find all known protein sequences that contain the pattern described by the regular expression from Q1. List the IDs of found proteins.
  3. Find all known protein structures that contain the pattern described by the regular expression from Q1. List the IDs of found protein structures.
  4. Build a multiple sequence alignment for all protein sequences from Q3.
  5. Change a single character in the regular expression from Q1 in such a way, that a search of protein sequence database for the pattern described by the modified regular expression would produce a larger number of hits than with the original regular expression.

( 3) CPRILMECKK  36

( 3) CPRILMECKR  34

( 6) CPRILMKCKK  39

( 3) CPRILMRCKR  42

( 2) CPRILMRCKQ  47

( 4) CPRIYMECKH  51

( 6) CPKILMECKK  46

( 3) CPRILMECSS  46

( 3) CPRILMECSS  46

( 3) CPRILMKCKH  39

( 2) CPRILMPCSS  50

( 4) CPRIYMECKR  48

( 3) CPRIWMECKR  43

( 3) CPLIWMECKR  74

( 3) CPKILMKCKH  49

( 4) CPKILMKCKQ  51

( 3) CPRIWMECTR  74

( 4) CPRILKQCKR 100

(37) CPRILMPCKT  51

(39) CPRILMPCKV  51