Difference Between BLAST and FASTA

Main Difference – BLAST vs FASTA

BLAST and FASTA are two similarity searching programs that identify homologous DNA sequences and proteins based on the excess sequence similarity. The excess similarity between two DNA or amino acid sequences arises due to the common ancestry-homology. The most effective similarity searching is the comparing of amino acid sequence of proteins rather than DNA sequences. Both BLAST and FASTA use a scoring strategy in order to compare two sequences and provide highly accurate statistical estimates about the similarities between sequences. The main difference between BLAST and FASTA is that BLAST is mostly involved in finding of ungapped, locally optimal sequence alignments whereas FASTA is involved in finding similarities between less similar sequences.    

Key Areas Covered  

1. What is BLAST
     – Definition, Programs, Uses
2. What is FASTA
     – Definition, Programs, Uses
3. What are the similarities between BLAST and FASTA
     – Common Features
4. What is the difference between BLAST and FASTA
     – Comparison of Key Differences

Key Terms: BLAST, FASTA, DNA, Nucleotide, Protein, Amino Acid, Homology, Similarity, Expectation Value

Difference Between BLAST and FASTA - Comparison SummaryWhat is BLAST

BLAST stands for Basic Local Alignment Search Tool. This searches for similarity between a query sequence and the sequences deposited in National Center for Biotechnology Information (NCBI) website. The putative genes in the query sequence can be detected based on the sequence homology of the deposited sequences. BLAST is popular as a bioinformatics tool due to its ability to identify regions of local similarity between two sequences quickly. BLAST calculates an expectation value, which estimates the number of matches between two sequences. It uses the local alignment of sequences. The NCBI BLAST web interface can be found here.

Difference Between BLAST and FASTA

Figure 1: NCBI BLAST Web Interface

Different BLAST Searches

BLAST program

Query and Database

BLASTN (nucleotide BLAST)

Query – Nucleotide, Database – Nucleotide

BLASTP (protein BLAST)

Query – Protein, Database – Protein


Query – Translated nucleotide, Database – Protein


Query – Protein, Database – Translated nucleotide


Query – Translated nucleotide, Database – Translated nucleotide

What is FASTA

FASTA is another sequence alignment tool which is used to search similarities between sequences of DNA and proteins. The query sequence is broken down into sequence patterns or words known as k-tuples and the target sequences are searched for these k-tuples in order to find the similarities between the two. FASTA is a fine tool for similarity searches. When finding sequence similarities, the best way to conduct your search is to first perform a BLAST search and then go to FASTA. The FASTA file format is widely used as the input method in other sequence alignment tools like BLAST. The web interface for FASTA, which is available at the European Bioinformatics Institute (EBI), can be found here

Main Difference - BLAST vs FASTA

Figure 2: FASTA Web Interface

FASTA Programs

FASTA Program



Protein – protein sequence comparison or nucleotide – nucleotide sequence comparison


Nucleotide – protein sequence comparison.


Local alignment between protein – protein or nucleotide – nucleotide sequence


Global alignment between protein – protein or nucleotide – nucleotide sequence


Global alignment of the query and local alignment of the sequences in the database.

Similarities Between BLAST and FASTA

  • BLAST and FASTA are two sequence comparison programs which provide facilities for comparing DNA and proteins sequences with the existing DNA and protein databases.
  • Both BLAST and FASTA are fast and highly accurate bioinformatics tools.
  • Both use pairwise sequence alignments.

Difference Between BLAST and FASTA


BLAST: BLAST is an algorithm for comparing primary biological sequence information like nucleotide or amino acid sequences.

FASTA: FASTA is a DNA and protein sequence alignment software package.

Stands for

BLAST: BLAST stands for Basic Local Alignment Search Tool.

FASTA: FASTA is short of “fast-all” or “FastA”.

Global/Local Alignment

BLAST: BLAST uses local sequence alignment.

FASTA: FASTA uses local sequence alignment first and then it extends the similarity search to global alignment.

Local Sequence Alignment

BLAST: BLAST searches similarities in local alignment by comparing individual residues in the two sequences.

FASTA: FASTA searches similarities in local alignments by comparing sequence patterns or words.

Type of Search

BLAST: BLAST is better for similarity searching in closely matched or locally optimal sequences.

FASTA: FASTA is better for similarity searching in less similar sequences. 

Type of Work

BLAST: BLAST works best for protein searches.

FASTA: FASTA works best for nucleotide searches.

Gaps in Query Sequence

BLAST: In BLAST, gaps between query and target sequences are not allowed.

FASTA: In FASTA, gaps are allowed.


BLAST: BLAST is a sensitive bioinformatics tool.

FASTA: FASTA is more sensitive than BLAST.


BLAST: BLAST is more speedy than FASTA.

FASTA: FASTA is less speedy toll when compared to BLAST.


BLAST: BLAST was designed by Stephen Altschul, Webb Miller, Warren Gish, Eugene Myers and David J. Lipman at the National Institute of Health in 1990.

FASTA: FASTA was developed by David J. Lipman and William R. Pearson in 1985.


BLAST: At present, BLAST is the most widely used bioinformatics tools for similarity searches.

FASTA: The legacy of FASTA is the FASTA format, which is now ubiquitous in bioinformatics.


BLAST and FASTA are two pairwise sequence alignment tools used in bioinformatics for searching similarities between DNA or protein sequences. BLAST is the most widely used tool for the local alignment of nucleotide and amino acid sequences. FASTA is a fine similarity searching tool which uses sequence patterns or words. It is best suited for the similarity searches between less similar sequences. The main difference between BLAST and FASTA is in the similarity searching strategies used in each tool.


1. Madden, Thomas. “The BLAST Sequence Analysis Tool.” The NCBI Handbook [Internet]. 2nd edition.U.S. National Library of Medicine, 15 Mar. 2013. Web.Available here. 09 June 2017. 
2. “Pairwise sequence alignment using FASTA.” Amrita Vishwa Vidyapeetham University. N.p., n.d. Web. Available here. 09 June 2017. 

Image Courtesy:

1.BLAST Official Site
2.FASTA Official Site

About the Author: Lakna

Lakna, a graduate in Molecular Biology and Biochemistry, is a Molecular Biologist and has a broad and keen interest in the discovery of nature related things. She has a keen interest in writing articles regarding science.

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