BLAST searching

Question 1

3 requirements for biological sequence database searching

Answer 1

Sensitivity (How correct it is)
Selectivity (Exclusion of incorrect hits)
Speed (How long it takes)

Question 2

Heuristics

Answer 2

Taking shortcuts for solving problems in a quick way that delivers a result that is sufficient enough to be useful given time constraints.

Question 3

Local vs global alignment

Answer 3

Local alignment identifies short regions of similarity detecting conserved domains within proteins. Global alignment compares sequences over their entire length, suitable for homologous genes with full-length conservation.

Question 4

Steps in BLAST algorithm

Answer 4

Read input sentence, generate word seeds, search database for matches, score matches based on substitution matrix, extend matches bidirectionally until score reaches lowest point.

Question 5

Scoring matrices in BLAST

Answer 5

BLOSUM-Blocks Substitution Matrix - based on conserved protein blocks
PAM-Point Accepted Mutation - based on evolutionary mutations over time.

Question 6

Blast programmes

Answer 6

BLASTN - nucleotide query and answer
BLASTP - protein query and answer
BLASTX - nucleotide query, protein answer
TBLASTN - protein query, nucleotide answer
TBLASTX - nucleotide (translated) query and answer.

Question 7

What is E value in BLAST results?

Answer 7

Score for how similar the answer is to the sequence of the query, the closer to 0 the better.

Question 8

Why are protein sequences preferred in BLAST?

Answer 8

Proteins are conserved, less mutations (bacteria).

Question 9

High scoring segment pairs (HSPs)

Answer 9

Ungapped local alignments between a query and a database sequence with scores above a predefined threshold.