Podcast
Questions and Answers
What is the first step in the BLAST algorithm?
What is the first step in the BLAST algorithm?
- Input Sequence and Database Selection (correct)
- Word Generation
- Output Results
- Scoring Alignments
What is the purpose of using a substitution matrix like BLOSUM in the BLAST algorithm?
What is the purpose of using a substitution matrix like BLOSUM in the BLAST algorithm?
- It is used to divide the query sequence into words.
- It accounts for variations among similar amino acids during word matching. (correct)
- It determines the alignment score based on gap penalties.
- It helps in estimating the E-value for alignments.
During the extension of matches in BLAST, what occurs when the alignment score drops below a certain threshold?
During the extension of matches in BLAST, what occurs when the alignment score drops below a certain threshold?
- The alignment is considered complete and is retained.
- The match is ignored and processing moves to the next word. (correct)
- The extension continues indefinitely until a perfect match is found.
- The scoring process is restarted from the beginning.
What are High-Scoring Segment Pairs (HSPs) in the context of the BLAST algorithm?
What are High-Scoring Segment Pairs (HSPs) in the context of the BLAST algorithm?
What does the E-value estimate in the BLAST algorithm?
What does the E-value estimate in the BLAST algorithm?
Flashcards
BLAST Input
BLAST Input
A query sequence (DNA, RNA, or protein) and a database to search against (like GenBank).
Word Generation (BLAST)
Word Generation (BLAST)
Dividing a query sequence into short, fixed-length subsequences (words).
Word Matching
Word Matching
Searching the database for exact or near-exact word matches (with substitutions for proteins).
BLAST Alignment Extension
BLAST Alignment Extension
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E-value (BLAST)
E-value (BLAST)
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Study Notes
BLAST Algorithm Steps
- The user provides a query sequence (DNA, RNA, or protein) and chooses a database (like GenBank) to search.
- The query sequence is broken down into short, fixed-length subsequences called words. Nucleic acid words might be 11 bases long, protein words 3 amino acids long.
- BLAST searches the database for words that are identical or similar to the query words. For proteins, a substitution matrix (like BLOSUM) factors in similar amino acid matches.
- When a matching word is found, BLAST extends the alignment in both directions until the alignment score falls below a certain threshold.
- Each alignment has a score based on substitution matrices and gap penalties (if gaps are present). High-scoring alignments become High-Scoring Segment Pairs (HSPs).
- The E-value is calculated to assess the statistical significance of each HSP—it estimates the probability the match was random.
- The results display HSPs with top scores (lowest E-values)--providing alignment regions, scores, and statistical significance.
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