Difference Between Blast and Fasta

Blast vs Fasta

Blast and Fasta are two software that are used to compare biological sequences of DNA, amino acids, proteins and nucleotides of different species and look for the similarities. These algorithms were written keeping speed in mind because as the data bank of the sequences swelled once DNA was isolated in the laboratory by the scientists in mid 1980s there raised a need to compare and find identical genes for further research at high speed. Blast is an acronym for Basic Local Alignment Search Tool and uses localized approach in comparing the two sequences. Fasta is a software known as Fast A where A stands for All because it works with the alphabet like Fast A for DNA sequencing and Fast P for protein. Both Blast and Fasta are very fast in comparing any genome database and are therefore very viable monetarily as well as in saving time.


One of the most widely used bioinformatics software Blast was developed in 1990 and since then have been available to everyone at NCBI site. This software can be accessed by any one and can be modified according to ones need. Blast is the software in which input data of a sequence to be compared is in Fasta format and output data can be obtained in plain text, HTML or XML. Blast works on the principle of searching for localized similarities between the two sequences and after short listing the similar sequences it searches for neighborhood similarities. The software searches for high number of similar local regions and gives the result after a threshold value is reached. This process differs from earlier software in which entire sequence was searched and compared which took a lot of time. Blast is used for many purposes like DNA mapping, comparing two identical genes in different species, creating phylogenetic tree.


Fasta program was written in 1985 for comparing protein sequences only but was later modified to conduct searches on DNA also. Fasta software uses the principle of finding the similarity between the two sequences statistically. This software matches one sequence of DNA or protein with the other by local sequence alignment method. It searches for local region for similarity and not the best match between two sequences. Since this software compares localized similarities at times it can come up with a mismatch. In a sequence Fasta takes a small part known as k-tuples where tuple can be from 1 to 6 and matches with k-tuples of other sequence and once a threshold value of matching is reached it comes up with the result. It is a program that is used to shortlist prospects of matching sequence from a large number for full comparison as it is very fast.

In brief:

Blast vs Fasta

• Blast is much faster than Fasta.

• Blast is much more accurate than Fasta.

• For closely matched sequences Blast is very accurate and for dissimilar sequence Fasta is better software.

• Blast can be modified according to the need but Fasta cannot be modified.

• Blast has to use Fasta input format to get the output data.

• Blast is much more versatile and widely used than Fasta.