Sequence Similarity Searching

Question 1

Sequence similarity

Answer 1

similiar physiochemical properties - common ancestry - common function

Question 2

Homology (and similarity)

Answer 2

share common ancestry (>80% similar)

Question 3

Homologous (2 types and meaning)

Answer 3

Orthologs - speciation event (similar functions)
Paralog- duplication avent (different functions)

Question 4

Sequence alignment and algorithms

Answer 4

enables maximisation of similarity, most likely evolutionary path

Question 5

Dynamic Programming Algorithms (allow what, 2 types, negative)

Answer 5

exhaustive identification of optimal alignments
too slow for large databases
global - whole sequence (~length)
local- local regions (biological relevance, find conserved patterns)

Question 6

Scoring alignment

Answer 6

quantification of similarity (what´s real from chance) - scoring matrix

Question 7

what represent gaps and mismatches

Answer 7

indels events relative to ancestor (mutations during replication)

Question 8

3 types of gap penalties formula

Answer 8

constant: -a
proportional to lenght: - (a x l)
affine gap: - (a+bl) a»b b= extending penalty proportional to gap length - more relevant

Question 9

formula of percentage of identically aligned residues

Answer 9

nº matches/length x 100

Question 10

protein alignments substitutions of aa are not equal why?

Answer 10

protein sequences are under stabilising selection for structure and function
depend on chemical similarity - similar aa substitute more easily
LEU>ILE or PRO>TRP

Question 11

BLOSUM62 substitution matrix

Answer 11

Gap free alignment of short protein motifs (BLOCKS)
Higher score - chemically similar, conservative (higher probability of homology)

Question 12

Heuristic Algorithms (vs DPAs) - example

Answer 12

high scoring short regions exact matches (break query into short words and look for matches and then see if can be extended)
faster
BLAST

Question 13

BLAST

Answer 13

all matches above threshold are extended until introduction of gaps
High scoring segment pairs (HSPs)
N - nt vs nt (gene)
P - protein vs protein (protein)
x- translated nt vs protein (DNA sequence code protein)
tblastn - protein vs translated nt (what DNA sequence encodes protein)

Question 14

p values
significant match p

Answer 14

probability of observing as high scoring an alignment between 2 unrelated sequences of similar length and composition
significant match - p<0,05

Question 15

Expect values (E)

Answer 15

how often a match at a given p value would be expected to occur in the database by chance (biologically unrelated) - threshold for significance
E= pX (should be =<0,01)
X- total length of all sequences in database/ length of aligned sequence

Question 16

DNA searches
Protein searches

Answer 16

DNA - evolutionary close
protein- distant