Quiz 1 - BINF

Question 1

What is the World wide protein data bank

Answer 1

has 3d structures of proteins, nucleic acids, ligand interactions, mutations links to other protein databases

Question 2

UniprotKB was

Answer 2

made by humans and has gene specific info and is validated but has no nucleotide sequences so protein focused

Question 3

THE NCBI has

Answer 3

a large but redundant amount, has genes and genomes of any organisms, mrna, jmicrorna, and anything that’s ever been sequenced do both proteins and nucleotides

Question 4

RefSeq is

Answer 4

large but not redundant, has genes and genomes, mrna microrna and is good for BLAST search, nucleotide focused

Question 5

FAST-A format is

Answer 5

a simple sequence that has meta-data

Question 6

BLAST stands for

Answer 6

basic local alignment search tool

Question 7

What is sequence alignment used for

Answer 7

to find sequence similarity, find common motifs, point mutations and insertions and deletions

Question 8

the three types of sequence alignments

Answer 8

Global, local, multiple

Question 9

What does global sequence alignment do?

Answer 9

Determines the best alignment over the entire length of two sequences

Best when sequences are similar

Question 10

What does local sequence alignment do?

Answer 10

looks at sequence stretches that are shorter than the entire thing
good for comparing really diff sequences with regions of similarity

Question 11

What does multiple sequence alignment do?

Answer 11

Aligns more than 2 sequences
good for when looking for conserved sequences of patterns in a protein family

Question 12

Math framework sequence alignment is good for

Answer 12

aiming to estblish residue-to-residue correspondances between sequences while preserving the order of other residues

Question 13

Math allows for

Answer 13

the into of Gaos so residue-to-nothing in a sequence

Question 14

Alignment scores, explain

Answer 14

Hoe to determine best sequence when aligning. matched are +1, mismatches and gaps -1

Question 15

So blast uses a match word to start alignment and

Answer 15

high scoring words are extended in either direction until alignment score drops

Question 16

s=
w=
p value =
e=

Answer 16

s= alignment score
w= word length
p value = probability that an alignment with a score greater or = to s occurred by chance
expectation cut-off (very small e means highly significant match)

Question 17

e must be at most

Answer 17

e e must be at most 1e-3 be at most 1e-3

Question 18

What makes Blast so quick?

Answer 18

`It doesnt try and extend or link discontinuos segments
doesn’t generate a global alignment
requires words to search
advanced programming

Question 19

The dayhoff (PAM) scoring matrix uses mutation. data matrix so

Answer 19

its dervived using PAM point accepted mutation

Question 20

What are gap penalties

Answer 20

making a gap is worst than extending one so making a gap is -5 while extending 1 is -1

Question 21

Howd they do that?

Answer 21

looked at proteins that were 85% identical and manually aligned, then calc the probability for each residue to change

Question 23

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