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2.4 Sequence File Formats — Test 1
Q1. In the FASTA format, each sequence record begins with a header line that starts with the symbol:✓ > (greater-than)
Q2. The GenBank flat-file format is characterised by including:✓ Rich annotation fields such as LOCUS, DEFINITION, FEATURES and ORIGIN
Q3. A major reason FASTA is so widely used is that it is:✓ Simple, plain-text and accepted by almost all tools
Q4. The .aln file produced by ClustalW (ClustalW2) stores:✓ A multiple sequence alignment
Q5. A multi-FASTA file is one that:✓ Contains several sequences, each with its own '>' header
Q6. The PIR (NBRF) format is another plain-text format used to store:✓ Protein (and nucleotide) sequences
Q7. The FASTQ format extends FASTA by additionally storing:✓ A per-base quality score for each nucleotide
Q8. The main practical reason standard sequence file formats matter is that they:✓ Allow data to be exchanged between different tools and databases
Q9. In a GenBank record, the actual nucleotide sequence appears after the keyword:✓ ORIGIN
Q10. Which format is most commonly required as input for a BLAST search?✓ FASTA
Q11. The header line of a FASTA record typically contains:✓ An identifier and a short description of the sequence
Q12. EMBL and GenBank flat-file formats both differ from FASTA mainly in that they:✓ Include extensive structured annotation alongside the sequence
Q13. Converting a sequence from GenBank format to FASTA format generally:✓ Keeps the sequence but discards most annotation
Q14. In FASTQ files, the quality scores are commonly encoded using:✓ ASCII characters representing Phred scores
Q15. The 3D structure of a protein is stored not in a sequence format but in a:✓ PDB file (atomic coordinates)
Q16. A practical benefit of FASTA's minimal structure is that it is:✓ Easy to parse and generate programmatically
Q17. The ClustalW alignment format shows, beneath the aligned sequences, symbols that indicate:✓ The degree of conservation at each column
Q18. When a tool reports it 'cannot read the input', a common fix is to:✓ Convert the sequence into the format the tool expects (e.g. FASTA)
Q19. A GenBank record is terminated by the symbol:✓ // (double slash)
Q20. Match each file format with its description and select the correct option.✓ A-iii, B-i, C-ii, D-iv