Question

Which file format includes both sequence and quality scores?

• A. FASTA
• B. GenBank
• C. FASTQ
• D. PDB

Hint:

Remember the common bioinformatics file formats: \[ \boxed{ \begin{aligned} \text{FASTA} &\rightarrow \text{Sequence Only} \\ \textbf{FASTQ} &\rightarrow \textbf{Sequence + Quality Scores} \\ \text{PDB} &\rightarrow \text{3D Structures} \end{aligned} } \] FASTQ is the standard output format of next-generation sequencing (NGS).

Answer 1

The Correct Option is C

Concept: Modern DNA sequencing technologies generate not only nucleotide sequences but also a quality score that indicates the confidence of each nucleotide read. The FASTQ file format was developed to store both the nucleotide sequence and its corresponding quality information in a single file.

Step 1: Understand the FASTQ format.
Each sequence entry in a FASTQ file consists of four lines:
• Sequence identifier (begins with @)
• DNA or RNA sequence
• Separator line (begins with +)
• Quality score string Thus, \[ \boxed{ \text{FASTQ} = \text{Sequence} + \text{Quality Scores} } \]

Step 2: Importance of quality scores.
Quality scores help researchers:
• Detect sequencing errors.
• Filter low-quality reads.
• Improve genome assembly.
• Increase confidence in downstream analyses. These scores are usually represented using ASCII characters based on the Phred quality scoring system.

Step 3: Eliminate incorrect options.

• FASTA stores only sequence information.
• GenBank stores annotated nucleotide records.
• PDB stores three-dimensional biomolecular structures.
• Only FASTQ stores both sequences and quality scores. Final Answer: \[ \boxed{Option (C) is correct \]