BLAST

Question 1

What does BLAST mean

Answer 1

basic local alignment search tool

Question 2

Who developed BLAST?

Answer 2

Altschul and colleagues

Question 3

algorithm for rapid searching of nucleotide and protein databases

Answer 3

BLAST

Question 4

employs a heuristic method of pairwise comparison

Answer 4

BLAST

Question 5

algorithm that estimates the best solution without considering every possible outcome

Answer 5

heuristic method

Question 6

does not guarantee to find best solutions but finds good solutions

Answer 6

heuristic method

Question 7

has high speed and is time efficient

Answer 7

heuristic method

Question 8

homologous sequence are likely to contain a short, high-scoring similarity region

Answer 8

BLAST Strategy

Question 9

short, high-scoring similarity region

Answer 9

word or hit (W)

Question 10

designed to find local regions of similarity but can be expected to run about two orders of magnitude faster than the Smith-Waterman algorithm

Answer 10

BLAST

Question 11

sequence that is subject to comparison

Answer 11

Query

Question 12

sequences showing similarity with the query sequence

Answer 12

subject (or target)

Question 13

What are different BLAST programs

Answer 13

blastn
blastp
blastx
tblastn
tblastx

Question 14

searches a nucleotide database using a nucleotide query

Answer 14

blastn

Question 15

searches a protein database using a protein query

Answer 15

blastp

Question 15

searches a protein database using a translated nucleotide query

Answer 15

blastx

Question 16

searches a translated nucleotide database using a protein query

Answer 16

tblastn

Question 17

searches a translated nucleotide database using a translated nucleotide query

Answer 17

tblastx

Question 18

if BLAST found a similar sequence, we must have an idea:

Answer 18

whether alignment is good
whether it portrays possible biological relationship
whether the similarity observed is attributable to chance alone

Question 19

uses statistical theory to produce a bit score and e-value

Answer 19

BLAST

Question 20

gives an indication of how good the alignment is

Answer 20

Bit Score

Question 21

In Bit score, the higher the score, _

Answer 21

the better

Question 22

key element in the calculation of bit score

Answer 22

substitution matrix

Question 23

bit score for the aligned region with the highest score

Answer 23

max score

Question 24

adds the bit scores for all aligned regions

Answer 24

Total score

Question 25

gives an indication fo the statistical significance of a given pairwise alignment and reflects the size of the database and the scoring system used

Answer 25

Expected value

Question 26

the lower the E-value, the _ is the hit

Answer 26

more significant

Question 27

determine the beginning and end positioning of genes in a genome

Answer 27

gene prediction problem

Question 28

determines the sequence of amino acids in a protein

Answer 28

sequence of codons

Question 29

What is the paradox of genome

Answer 29

Genome size of many eukaryotes does not correspond to genetic complexity

Question 30

When was the discovery of split genes through experiments with mRNA of hexon, a viral proteins

Answer 30

1977

Question 31

When was it discovered that the sequence of codons in a gene determines the sequence of amino acids in a protein

Answer 31

1960s

Question 32

True or False: the genome of many eukaryotes contain only relatively few genes

Answer 32

True

Question 33

Problems in Gene Prediction

Answer 33

genome has relatively few genes many false splice short exons long introns alternative splicing