Question

Arrange the given steps in BLAST procedure using a hypothetical Query in order of their occurrence. A. Calculate sum of match scores based on substitution matrix for the matched word, B. Find the database sequence corresponding to the best word match and extend alignment in both directions, C. Creation of every three residue words from the query sequence and scan them searching in BLAST word database, D. Determine high scored segment above threshold, E. Input query sequence.

• A. A, B, C, D, E
• B. A, E, B, C, D
• C. E, C, A, B, D
• D. E, D, C, B, A

Hint:

BLAST procedure starts with query input, then word generation, scoring, extension of alignment, and finally identification of high scoring segments.

Answer 1

The Correct Option is C

Concept:
BLAST is a sequence similarity search tool. It compares a query sequence with sequences present in a database and identifies regions of local similarity.

Step 1: Input query sequence.
The BLAST process starts when the user enters a query sequence. This may be a DNA sequence, RNA sequence, or protein sequence. \[ \text{First step} = E \]

Step 2: Create words from query sequence.
BLAST breaks the query sequence into short words. For protein BLAST, words of three residues are commonly considered. \[ \text{Second step} = C \]

Step 3: Calculate match scores.
The words are compared using a substitution matrix. The sum of match scores is calculated for matched words. \[ \text{Third step} = A \]

Step 4: Find database sequence and extend alignment.
BLAST finds the best matching words in database sequences and extends the alignment in both directions. \[ \text{Fourth step} = B \]

Step 5: Determine high scoring segment.
Finally, high scoring segment pairs above the threshold are identified. \[ \text{Fifth step} = D \] Therefore, the correct sequence is: \[ E, C, A, B, D \] \[ \therefore \text{Correct Answer is (C)} \]