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3.2 Database Searching: BLAST & FASTA — Test 1
Q1. BLAST stands for:✓ Basic Local Alignment Search Tool
Q2. The BLAST program 'blastp' is used to search:✓ A protein query against a protein database
Q3. The BLAST program 'blastn' compares:✓ A nucleotide query against a nucleotide database
Q4. The BLAST program 'blastx' searches:✓ A translated nucleotide query against a protein database
Q5. PSI-BLAST is particularly valuable because it can:✓ Detect distantly related (weak) homologues using iterative profiles
Q6. In BLAST output, the E-value (expectation value) represents the:✓ Number of hits of similar quality expected purely by chance
Q7. A BLAST hit with an E-value of 1e-50 compared with one of 0.5 is:✓ Far more statistically significant
Q8. BLAST is described as a heuristic algorithm because it:✓ Trades guaranteed optimality for speed, finding good (not always optimal) alignments
Q9. BLAST works by first finding short matching segments called:✓ Words (or seeds)
Q10. The BLAST program 'tblastn' searches:✓ A protein query against a translated nucleotide database
Q11. The FASTA algorithm, like BLAST, is a:✓ Heuristic method for fast database searching
Q12. The bit score reported by BLAST is useful because it is:✓ A normalised score independent of database size
Q13. Choosing the correct BLAST program depends mainly on:✓ Whether the query and database are nucleotide or protein
Q14. A key reason BLAST is preferred over a full Smith-Waterman search of a large database is that BLAST is:✓ Much faster while still highly sensitive
Q15. The 'nr' database often searched with BLAST is the:✓ Non-redundant sequence database
Q16. A very high E-value (e.g. 10) for a BLAST hit indicates that the match is:✓ Likely to have occurred by chance (not significant)
Q17. BLAST results typically report percent identity and:✓ Query coverage (how much of the query is aligned)
Q18. Compared with BLAST, the FASTA program is generally:✓ Sometimes more sensitive but typically slower
Q19. The main inputs a user must provide for a BLAST search are the:✓ Query sequence and the database to search
Q20. Match each BLAST program with its query/database type and select the correct option.✓ A-iii, B-i, C-ii, D-iv