L3

Question 1

Retrieval of biological sequences in databases is based on what?

Answer 1

Similarity

Question 2

Searching biological sequence databases involves?

Answer 2

Submission of a query sequence and performing a pairwise comparison query with all individual sequences in a database

Question 3

Requirements for implementing algorithms for sequence database searching include

Answer 3

• sensitivity
• selectivity
• speed

Question 4

Sensitivity

Answer 4

Refers to the ability to find as many correct hits as possible. The correct hits are considered true positives

Question 5

Selectivity

Answer 5

also called specificity, which refers to the ability to exclude incorrect hits. These
incorrect hits are considered “false positives.”

Question 6

Speed

Answer 6

which is the time it takes to get results from database searches

Question 7

An increase in sensitivity leads to

Answer 7

a decrease in selectivity

Question 8

an increase in speed leads to

Answer 8

a decrease in sensitivity and selectivity

Question 9

What are the types of algorithms in database searching

Answer 9

• exhaustive
• heuristic

Question 10

Exhaustive algorithm

Answer 10

makes use of a rigorous algorithm to find the best or exact solution for a particular problem by examining all mathematical combinations

Question 11

Heuristic algorithm

Answer 11

a computational strategy to find the near optimal solution

Question 12

How do heuristic algorithms take shortcuts

Answer 12

by reducing space according to some criteria

Question 13

what are the methods used to infer sequence similarity

Answer 13

Global and Local alignment

Question 14

Local alignment

Answer 14

Finds domains and short regions of similarity between a pair of sequences eg
-looking for domains within proteins
-looking for regions of genomic DNA that contain introns

Question 15

Global alignment

Answer 15

Finds the optimal alignment over the entire length of the two sequences under comparison eg
-genes are being aligned whose sequences are of comparable length
-entire gene is homologous

Question 16

what does BLAST stand for

Answer 16

Blasic Local Alignment Search Tool

Question 17

How does BLAST work

Answer 17

It uses heuristics to align a query sequence with all sequences in a database. Its objective is to find high-scoring segments among related sequences.

Question 18

How does BLAST perform sequence alignment

Answer 18

1. reads in query sequence
2. Create a list of words from the query sequence (seeding) 3 RESIDUES FOR PROTEIN, 11 FOR DNA SEQUENCES
3. Search a sequence database for the occurrence of these words.
4. matching of the words is scored by a given substitution matrix
5. Pairwise alignment

Question 19

The resulting contiguous aligned segment pair without gaps is called what

Answer 19

high-scoring segment pair

Question 20

Database search programs such as BLAST use

Answer 20

scoring/substitution matrices

Question 21

Scoring matrices are what

Answer 21

empirical weighting schemes

Question 22

Possible identities and substitutions are assigned a score based on the?

Answer 22

observed frequencies of such occurrences in alignments of related proteins

Question 23

What does BLASTN do

Answer 23

queries nucleotide sequences with a nucleotide sequence database

Question 24

How does BLASTP work

Answer 24

uses protein sequences as queries to search against a protein sequence
database. Default word size is 3

Question 25

How does BLASTX work

Answer 25

uses translated nucleotide sequences as queries which are used to query a protein sequence database.

Question 26

How does TBLASTN

Answer 26

queries protein sequences to a nucleotide sequence database with the DNA sequences translated.

Question 27

How does TBLASTX work

Answer 27

uses nucleotide sequences, which are to search against a nucleotide sequence database that has all the sequences translated also

Question 28

What is BLAST used for?

Answer 28

- to detect similarity between sequences of interest. - to determine whether there are other plausible alignments between query and target sequences

Question 29

What is the BLAST E-value

Answer 29

it provides information about the likelihood that a given sequence match is purely by chance. The lower the E-value, the less likely the database match is a result of random chance.

Question 30

HSPs significances are determined by Blast using the Karlin-Altschul equation

Answer 30

E = kmNe -lamda(s)

Question 31

E stands for

Answer 31

the expectation value

Question 32

k and lamda are what?

Answer 32

Karlin-Altschul constants

Question 33

m stands for

Answer 33

the number of letters (amino acids/nucleotides) in the query

Question 34

N is the

Answer 34

the total number of letters (aa/nuc) in the database

Question 35

If E < 1e− 50 (or 1 × 10−50),

Answer 35

there should be an extremely high confidence that the database match is a result of homologous relationships.

Question 36

If E is between 0.01 and 1e− 50,

Answer 36

the match can be considered a result of homology

Question 37

If E is between 0.01 and 10,

Answer 37

the match is considered not significant, but may hint at a tentative remote homology relationship.

Question 38

If E > 10,

Answer 38

the sequences under consideration are either unrelated or related by extremely distant relationships that fall below the limit of detection with the current method.