What is the Difference Between FASTA and FASTQ

The key difference between FASTA and FASTQ is that FASTA is a text-based format that only stores nucleotide or protein sequences, while FASTQ is a text-based format that stores both sequence and associated sequence quality values.

Bioinformatics is a field that uses different software to analyse and understand biological data, especially when the set of data is complex and large. This field combines biology, chemistry, physics, computer science, information engineering, mathematics, and statistics to analyze and interpret biological data. FASTA and FASTQ are two sequence representation formats in the field of bioinformatics to align and analyse sequences. In fact, FASTQ is a sequence file format that extends the FASTA format with the ability to store the sequence quality.

CONTENTS

1. Overview and Key Difference
2. What is FASTA
3. What is FASTQ
4. Similarities – FASTA and FASTQ
5. FASTA vs FASTQ in Tabular Form
6. Summary – FASTA vs FASTQ

What is FASTA?

FASTA is an alignment software for DNA and protein sequence. FASTA software uses FASTA format. It is a text-based format that represents either nucleotide sequences or amino acid (protein) sequences. Here, single letter codes represent both these sequences. FASTA is an important tool in the fields of bioinformatics and biochemistry. This format allows for sequence names and comments to precede the sequences.

FASTA vs FASTQ in Tabular Form

Figure 01: FASTA Sequence

This format originated from the FASTA software and was introduced by David J. Lipmann and William R. Pearson in 1985. The FASTA tool had many modifications over time, and the latest version consists of programs for protein:protein, DNA:DNA, protein:translated DNA (with frameshifts) and ordered or unordered peptide searches. FASTA reads a given nucleotide or amino acid sequence and looks for the corresponding sequence database by using local sequence alignment to find matches of similar database sequences.

What is FASTQ?

FASTQ is an alignment software used in the field of bioinformatics, which stores both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. FASTQ was originally developed to bundle a FASTA formatted sequence and the related quality data by Wellcome Trust Sanger Institute. With the development in the field of bioinformatics, FASTQ became the de facto standard for storing the output of many high-throughput sequencing instruments.

The FASTQ format uses four different lines per sequence. Line 1 begins with @ character and is followed by a sequence identifier (similar to a FASTA title line). Line 2 consists of raw sequence letters. In line 3, the sequence begins with a ‘+’ character and is optionally followed by the same sequence identifier. Line 4 encodes the quality values for the sequence in line 2 and should consist of the same number of symbols as letters in the sequence.

What are the Similarities Between FASTA and FASTQ?

  • FASTA and FASTQ are alignment tools.
  • They are two sequence representation formats.
  • Both are related to the field of bioinformatics.
  • Both FAST and FASTQ are important tools for storage and sequencing purposes.
  • FASTQ is an extension of the FASTA format with the ability to store the sequence quality.

What is the Difference Between FASTA and FASTQ?

FASTA is a text-based format that stores only nucleotide or protein sequences, while FASTQ is a text-based format that stores both sequence and associated sequence quality values. Thus, this is the key difference between FASTA and FASTQ. Moreover, FASTA stores sequence fragments after being mapped, while FASTQ stores sequence fragments before mapping. Besides, another difference between FASTA and FASTQ is that FASTA consists of one description line, and FASTAQ consists of four lines.

The below infographic presents the differences between FASTA and FASTQ in tabular form for side-by-side comparison.

Summary – FASTA vs FASTQ

Bioinformatics uses different formats of sequences such as FASTA and FASTQ, etc. FASTA stores sequence fragments after being mapped while FASTQ stores the sequence fragments before mapping. FASTA is an alignment software for DNA and protein sequence. It consists of programs for protein:protein, DNA:DNA, protein:translated DNA (with frameshifts), and ordered or unordered peptide searches. FASTQ is an alignment software used in the field of bioinformatics and stores both a biological sequence (usually nucleotide sequence) and its corresponding quality scores. FASTA consists of one description line, and FASTQ consists of four lines. So, this summarizes the difference between FASTA and FASTQ.

Reference:

1. Akalin, Altuna. “Computational Genomics with R.” 7.1 FASTA and FASTQ Formats.
2. “Fasta Format Description.” National Center for Biotechnology Information, U.S. National Library of Medicine.

Image Courtesy:

1. “Histone Alignment” By Thomas Shafee – Own work (CC BY 4.0) via Commons Wikimedia

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