IV - Bioinformatics

Gaps

• position at which a letter is paired with a null

• typically negative

• gap presence is more important then the length

BLOSUM

Blocks Substitution matrix

Blosum 62

Is a matrix calculated from comparisons of sequences w/ no less than 62% divergence

• default in BLAST

Alignment scoring is required

• + or - values

• gap creation and extension penalties

• positive scores are identities

• some partial positive score

• global vs local

• sub matrix

Global Alignment

• extends from one end to another

• finds optimal alignments between 2 sequences, gaps are permitted

• total length is aligned

Local Alignment

• matches regions within a sequence

• alignment can contain just a portion

• is appropriate for finding matched domains

BLAST

• Basic Local Alignment Search Tool

• allows for rapid sequence comparison

• Fast, accurate

• provides database of seq alignments along with E value

E value

Estimate that a sequence alignment occured by chance

BLAST Application

• identifying ortho/paralogs

• discovering new genes and proteins

• discovering variants

• investigating EST

• exploring protein structure functions

Homologs

2 molecules that are derived from a common ancestor

Orthologs

homologs that are present within different species have similar functions

Paralogs

homologs that are present within one species and often differ in their functions

✦ Only 16% sequence identities

Divergent evolution

process by which proteins derived from a common ancestor accumulate differences over time

Sequence alignment

Process of systematically aligning 2 sequences w/ respect to each other in order to identify regions of specific overlap.

✦ If the alignment score is higher than the scores gotten by random shuffling, it proves that the alignment was likely not by chance

Gap

Sequence is split and pushed to maximize alignment. Each identity (identical AA) betweened aligned sequences is +10 points. Each gap is -25 points.

Substitution matrix

scoring system based on replacing an AA by 19 others.

✦ large +ve score = frequent substitution

✦ large -ve scre = rare substitution

Conservative v.s. Non-conservative substitutions

✦ similar in size/chemical properties will occur more often, it may have minor effects on proteins

✦ AA is structurally dissimilar, may disrupt structure & function

see Blosum-62

Convergent evolution

Proteins don’t have the same ancestor but are converging to the same function

What are the alignment score and percent identity?

Alignment score = (6 × 8) - 15 = 33

Percent identity: 6/13 = 46% or 6/14 = 43%