Journal of Medicinal Plants Research Vol. 5(32), pp.

6931-6933, 30 December, 2011

Available online at http://www.academicjournals.org/JMPR
ISSN 1996-0875 ©2011 Academic Journals
DOI: 10.5897/JMPR11.363

Review

Fast alignment (FASTA): A review article

M. Akram1*, M. Saim Jamil1, Zahid Mehmood2, Muhammad Akram5,
Muhammad Khurram Waqas4, Zafar Iqbal3, Aubid Allah Khan3 and H. M. Asif3
1
Shifa ul Mulk Memorial Hospital, Hamdard University, Karachi, Pakistan.
2
Department of Chemistry and Biochemistry, University of Agriculture Faisalabad-38040, Pakistan.
3
Department of Pharmacy, The Islamia University of Bahawalpur, Pakistan.
4
Department of Pharmacy, The University of Faisalabad, Pakistan.
5
Department of Pharmacy, University of Sargodha, Pakistan.
Accepted 4 October, 2011

Fast alignment (FASTA) is used to compare protein sequence to another protein sequence. FASTA
provides similarity between nucleotide and protein databases using the FASTA program. FASTA is
usually used as part of a package of programs and it construct local and global sequence alignments.
In this article, simple applications of FASTA were discussed.

Key words: Fast alignment (FASTA), program, sequence similarity.

INTRODUCTION

Fast alignment (FASTA) is a program that is utilized to
analyze the similarity between protein sequences as well
as nucleic acids. It also searches protein and DNA
databases and finds similarities between them. This
program is used to find the region of similarity, local as
well as global. FASTA is both fast and selective because
it initially considers only amino acid identities.This
program may help in understanding evolutionary
relationships between sequences as well as help identify
members of gene families (Harison, 2005). The FASTA
program can search the NBRF (National Biomedical
Research Foundation) protein sequence library (2.5
million residues) in less than 20 min on an IBM-PC
(International Business Machines Corporation Personal
Computer) microcomputer and unambiguously detect
proteins that shared a common ancestor billions of years
in the past (Mackey et al., 2002, Pearson, 1990).
Computers are commonly used for analyses of DNA and
protein sequence data. A common application of
computers in molecular biology is to characterize newly
determined sequences by searching for DNA and protein
sequence databases. FASTA is widely used for such type
of searches, because it is fast, sensitive, and readily
available (Table 1). FASTA is used for local as well as
global alignment purposes (Henikoff et al., 1992, Brenner
et al., 1998). The present study focuses on the steps
required to run the programs, rather than on the
interpretation of the results of a FASTA search.
FASTA
Sequence similarity search using the FASTA
program
The uses of FASTA in databases include protein,
nucleotide, proteomes, genomes, whole genome
shotgun, ASD (Alternative splicing database) protein A,
SD (Splicing database) nucleotide, LGIC (Ligand-Gated
Ion Channel) protein and LGIC nucleotide.
FASTA program
FASTA-protein similarity search
This tool provides sequence similarity searching for
protein databases using the FASTA program (Pearson et
al., 1998). The steps to follow are:

1. Protein sequence is obtained from Uniprot

knowledgebase,
*Corresponding author. E-mail: makram_0451@hotmail.com. 2. Sequence is uploaded in FASTA soft ware,
Tel: 92 021 6440083. Fax: 92 021 6440079. 3. Parameters for analysis are set,
6932 J. Med. Plants Res.
Table 1. File extension
S/N Extension
1 Fasta
2 Fna
3 Ffn
4 Faa
5 Frn
4. Submit option is clicked,
5. Results are obtained after few minutes.
Protein and DNA/RNA databases
Numerous databases of protein have been developed.
Swissprot is an example.
FASTA-based compilation of higher plant
mitochondrial tRNA genes
FASTA program for similarity searching in nucleotide
sequence databases has been developed by means of
the FASTA program. New version of the compilation of
higher plant mitochondrial tRNA genes has been
obtained. Previous collection has been improved upon.
158 sequences with an increase of 43 units are in current
compilation (Sagliano et al., 1998).
BIOFFORC (Biological file format conversion) tool
development for biological file format
Different sequence formats are used in bioinformatics.
Specific sets of bioinformatics are used for processing.
Sometimes, sequence format conversion is needed. In
the public domain there are many sequence conversion
tool present. For this purpose a file format converter has
been developed with a graphical user interface in PERL
(Practical Extraction and Report Language). This file
format converter is called BIOFFORC (Chinnaiah et al.,
2008).
Using the FASTA program to search protein and DNA
sequence databases
Computers are commonly used for analysis of DNA and
protein sequence data. Newly determined sequences are
characterized by searching DNA and protein sequence
databases. The FASTA program is commonly used for
such searches due to its fastness and sensitivity. Steps
to run the FASTA programs have been developed
Meaning
Generic fasta
Fasta nucleic acid
FASTA nucleotide coding regions
Fasta amino acid
FASTA non coding RNA
DISCUSSION
FASTA is used for rapid alignment of pairs of protein and
DNA sequences. This program searches for matching
sequence patterns or words, called k-topples. These
patterns comprise k consecutive matches of letters in
both sequences (Juke, 1998). The program attempts to
build a local alignment based on these word matches
(Altschul and Gash, 1996). Due to the ability of the
algorithm to find matching sequences in a sequence
database with high speed, FASTA is useful for routine
database searches of this type. Other programs like
BLAST (Basic local alignment sequence tool) is faster
than FASTA, and is of comparable sensitivity for protein
queries; and also does DNA searches. Programs that use
the Smith-Waterman dynamic programming algorithm for
protein and DNA searches are slower but more sensitive
when full-length protein sequences are used as queries
(Lipan et al., 1984).
CONCLUSION
FASTA is commonly used for comparing sequences of
protein and DNA. It gives fast and reliable results. FASTA
provides an estimate of the statistical significance of each
alignment found.
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Brenner SE, Chothia C, Hubbard TJ (1998). Assessing sequence
comparison methods with reliable structurally identified distant
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Harison S (2005). FASTA, Fundamentals of Bioinformatics, I.K.
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Henikoff S, Henikoff JG (1992). Amino acid substitution matrices from
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