Motif Search

The Brute-Force Motif Search

Task 1

• In R, create a function Score(), that calculates the score for a consensus string.

• Input:

  • an array of starting indexes
  • DNAStringSet of sequences (for example file seq_score.fasta)
  • motif length

• Output:

  • the score for the consensus string

Task 2

• In R, create function NextLeaf() according to the following pseudocode.

• Input:

  • s = (s1 s2 … st); an array of starting indexes, where t is the number of sequences
  • t; number of DNA sequences
  • k = n - l + 1, where n is length of DNA sequences and l is motif length

• Output:

  • an array of starting indexes that corresponds to the next leaf in the tree

NextLeaf(s, t, k)
1   for i ← t to 1
2     if s[i] < k
3       s[i] ← s[i] + 1
4       return s
5     s[i] ← 1
6   return s

Task 3

• In R, create a function BFMotifSearch() according to the following pseudocode.

• Input:

  • DNA; DNAStringSet of DNA sequences (for example file seq_motif.fasta)
  • t; number of DNA sequences
  • n; length of each DNA sequence
  • l; motif length

• Output:

  • an array of starting positions for each DNA sequence with the best score for the consensus string

BFMotifSearch(DNA, t, n, l)
1   s ← (1, 1, ... , 1)
2   bestScore ← Score(s, DNA, l)
3   while forever
4     s ← NextLeaf(s, t, n − l + 1)
5       if Score(s, DNA, l) > bestScore
6         bestScore ← Score(s, DNA, l)
7         bestMotif ← (s1, s2, . . . , st)
8       if s = (1, 1, . . . , 1)
9         return bestMotif

The Branch-and-Bound Motif Search

Task 4

• In R, create a function NextVertex() according to the following pseudocode.

• Input:

  • s = (s1 s2 … st); an array of starting indexes, where t is the number of sequences
  • i; level of vertex
  • t; number of DNA sequences
  • k = n - l + 1, where n is length of DNA sequences and l is motif length

• Output:

  • the next vertex in the tree
  • current level of vertex

NextVertex(s, i, t, k)
1   if i < t
2     s[i + 1] ← 1
3     return (s, i + 1)
4   else
5     for j ← t to 1
6       if s[j] < k
7         s[j] ← s[j] + 1
8         return (s, j)
9   return (s, 0)

Task 5

• In R, create a function ByPass() according to the following pseudocode.

• Input:

  • s = (s1 s2 … st); an array of starting indexes, where t is the number of sequences
  • i; level of vertex
  • t; number of DNA sequences
  • k = n - l + 1, where n is length of DNA sequences and l is motif length

• Output:

  • the next leaf after a skip of the subtree
  • current level of vertex

ByPass(s, i, t, k)
1   for j ← i to 1
2     if s[j] < k
3       s[j] ← s[j] + 1
4       return (s, j)
5   return (a, 0)

Task 6

• In R, create a function BBMotifSearch() according to the following pseudocode.

• Input:

  • DNA; DNAStringSet of DNA sequences (for example file seq_motif.fasta)
  • t; number of DNA sequences
  • n; length of each DNA sequence
  • l; motif length

• Output:

  • an array of starting positions for each DNA sequence with the best score for the consensus string

• Modify function Score() to calculate a partial consensus score for first i rows of DNA.

BBMotifSearch(DNA, t, n, l)
1   s ← (1, ... , 1)
2   bestScore ← 0
3   i ← 1
4   while i > 0
5     if i < t
6       optimisticScore ← Score(s, i, DNA, l) + (t - i) * l
7       if optimisticScore < bestScore
8         (s, i) ← ByPass(s, i, t, n - l + 1)
9       else
10        (s, i) ← NextVertex(s, i, t, n − l + 1)
11    else
12      if Score(s, t, DNA, l) > bestScore
13        bestScore ← Score(s, t, DNA, l)
14        bestMotif ← (s1, s2, ... , st)
15      (s, i) ← NextVertex(s, i, t, n − l + 1)
16  return bestMotif

Download files from GitHub

Basic Git settings

• Configure the Git editor

  git config --global core.editor notepad

• Configure your name and email address

  git config --global user.name "Zuzana Nova"
  git config --global user.email [email protected]

• Check current settings

  git config --global --list

• Create a fork on your GitHub account. On the GitHub page of this repository find a Fork button in the upper right corner.

• Clone forked repository from your GitHub page to your computer:

git clone <fork repository address>

• In a local repository, set new remote for a project repository:

git remote add upstream https://github.com/mpa-prg/exercise_07.git

Send files to GitHub

Create a new commit and send new changes to your remote repository.

• Add file to a new commit.

git add <file_name>

• Create a new commit, enter commit message, save the file and close it.

git commit

• Send a new commit to your GitHub repository.

git push origin main