Question

Identify the correct sequence steps used by BLAST: A. A list of word of length 3 is made in the query sequence. B. Threshold step is repeated for each three-letter word in the query sequence. C. Sequence is optionally filtered to remove low complexity region. D. Threshold is selected to reduce the number of possible matches. E. Each database is scanned for exact match to one of the 50 words.

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

Hint:

In BLAST, first filter the query, then generate words, apply threshold, repeat scoring for words, and scan the database for matches.

Answer 1

The Correct Option is C

Concept:
BLAST is a sequence alignment tool used to find local similarity between a query sequence and database sequences. It works by breaking the query into short words and searching for high-scoring matches.

Step 1: Filter low complexity regions.
Before searching, the query sequence may be filtered to remove low complexity regions. These regions can produce false or meaningless matches. \[ \text{First step} = C \]

Step 2: Make words from query sequence.
For protein BLAST, words of length 3 are commonly generated from the query sequence. \[ \text{Second step} = A \]

Step 3: Select threshold.
A threshold score is selected so that only meaningful possible matches are considered. \[ \text{Third step} = D \]

Step 4: Repeat threshold step.
The threshold checking is repeated for each three-letter word in the query sequence. \[ \text{Fourth step} = B \]

Step 5: Scan database.
The database is scanned to find exact or high-scoring matches with the query words. \[ \text{Fifth step} = E \] Therefore, the correct sequence is: \[ C, A, D, B, E \] \[ \therefore \text{Correct Answer is (C)} \]