Basic Local Alignment Search Tool (BLAST)

Question 1

main NCBI tool for comparing a protein or DNA sequence (query) to other database sequences (target) = reveals related sequences

finds regions of local similarity between sequences having both speed and sensitivity (heuristic local alignment)

Answer 1

Basic Local Alignment Search Tool (BLAST)

Question 2

BLAST algorithm

1. For the query find the list of high scoring words of length w
2. Compare the word list to the database and identify exact matches.
3. For each word match, extend alignment in both directions to find alignments that score greater than score threshold S.

Question 3

BLAST: Uses

Answer 3

1. Determining what orthologs and paralogs are known for a particular protein or nucleic acid sequence.
2. Determining what proteins or genes are present in a particular organism.
3. Determining the identity of a DNA or protein sequence.
4. Discovering new genes.
5. Determining what variants have been described for a particular gene or protein.
6. Investigating expressed sequence tags (ESTs) that may exhibit alternative splicing.
7. Exploring amino acid residues that are important in a protein’s function and/or structure.

Question 4

BLAST: 4 Key Steps

Answer 4

1. Specifying Sequence of Interest
2. Selecting BLAST Program
3. Selecting a Database
4. a: Selecting Optional Search Parameters
   b: Selecting Formatting Parameters

Question 5

What program to use to compare a protein query to a database of proteins.

Answer 5

BLASTP

Question 6

What program to use to compare both strands of a DNA query against a DNA database

Answer 6

BLASTN

Question 7

What program to use to translate a DNA sequence into 6 protein sequences using all 6 possible reading frames, and then compare each of these proteins to a protein database

Answer 7

BLASTX

Question 8

What program to use to translate every DNA sequence in a database into 6 potential proteins, and then compare the protein query against each of those translated proteins.

Answer 8

TBLASTN

Question 9

What program is the most computationally intensive BLAST algorithm. It translates DNA from both a query and a database into 6 potential proteins, then performs 36 protein-protein database searches.

Answer 9

TBLASTX

Question 10

BLAST: Search Statistics

the number of different alignments with scores equivalent to or better than S (similarity score) that are expected to occur by chance in a database search; affected by the scoring system, size of the database, and size of the query

Answer 10

E = expect value

Question 11

probability of a chance alignment occurring with the score in question or better; closer to zero the better

Answer 11

p-value