sequence alignment

Question 1

bioinformatics resources

Answer 1

• algorithm
  
  • set of rules to perform an operation
  • same one can be used by different programs
• program
  
  • code that implements an algorithm
  • can use stored data, but not its aim (e.g. PSI BLAST)
• database
  
  • organised searchable source of biological data
  • aim is to store data

Question 2

protein evolution

Answer 2

• duplication can lead to divergent evolution
  
  • homologous proteins with related sequences and structures
  • often but not always related function
• analyse by alignment

Question 3

alignment features

Answer 3

• identity (:)
• gap
  
  • insertion or deletion
• substitution
  
  • can be conservative (.)
  • same characteristics e.g. hydrophobicity
• end gap
  
  • one sequence longer than the other

Question 4

paralogs

Answer 4

• homolog created by gene duplication within a species
• can result in change of function
  
  • original copy can maintain function
  • second copy free to mutate and adopt novel function

Question 5

orthologs

Answer 5

• homolog created by speciation
• both species now have a single copy of the same gene
• only one copy per species
  
  • less likely to change
  • function needs to be retained

Question 6

requirements of a pairwise protein sequence alignment

Answer 6

• scoring scheme of residue similarity
• algorithm to establish the alignment
• aim to combine algorithm and scoring scheme to generate the best alignment in biological terms
• potential to be extended to database searching

Question 7

scoring schemes

Answer 7

• simplest would be 1 for identity and 0 for different
• better to include similarity of residues
  
  • conservative subsitutions indicate more recent changes
  • residues tend to retain chemical properties so that function is modified, not destroyed
• gaps also indicate increased distance

Question 8

BLOSUM

Answer 8

• blocks substitution matrix
• aligned segments of protein families (blocks)
• blosum62:
  
  • clustered sequences in blocks where pairwise identity >62%
  • most widely used

Question 9

blosum62

Answer 9

• substitution matrix
  
  • score for changing one residue to another
  • represents chemical similarity
• e.g. cys - disulfide formation means high conservation
  
  • presence in both sequences indicate similarity
  • high score (9)
• low negative score if properties change
  
  • e.g. hydrophobic to charged
• empirical
• gaps considered later

Question 10

affine gap penalty

Answer 10

• penalise insertions/deletions
• penalty = o + el
  
  • o = gap opening constant
  • e = gap extension constant
  • l = length of gap extension
• o>e
  
  • gap introduction is the major event
  • extending the gap is minor

Question 11

protein domains

Answer 11

• protein seqeucnes formed of domains
• each domain originates from a different homologous family
• domains are the evolutionary unit
• methods need to take this into account
  
  • don’t have to align whole sequence

Question 12

local vs global alignment methods

Answer 12

• different algorithms
• part or all of a query can match part or all of a database sequence
• gaps may be needed to get a suitable alignment

Question 13

dotplot

Answer 13

• used to assign identities
• one sequence on each axis
• assign dot where they match along the diagonal
• best path has the highest number of dots
• need closely related sequences

Question 14

needleman wunsch algorithm

Answer 14

• dynamic programming
• maximises similarity score to give maximum match
  
  • largest number of residues of one sequence that can be matched with another allowing for all possible insertions/deletions
• finds best global alignment
• iterative matrix method
  
  • 2D array of all possible pairs of residues (bases or amino acids)
  • one sequence on each axis
  • all possible alignments represnted by paths through the array

Question 15

NW similarity values

Answer 15

• S_ij = numerical value assigned to every cell in the array
• depends on similarity of the 2 residues
• value of 1 indicates identity

Question 16

NW alignment construction

Answer 16

• add Sij from left to right along a path through the array to get cumulative alignment score
• best alignment has highest score = maximum match
  
  • maximum match always in outer row/column
  • work backwards from here to construct alignment
  • gaps can be inserted

Question 17

smith waterman algorithm

Answer 17

• compares segments of all possible lengths instead of looking at each sequence as a whole
  
  • local alignment
• choose whichever maximises similarity measure
• allow for gaps
• variation on NW
  
  • dynamic programming