This document provides an overview of the FASTA software. FASTA is a program used by biologists to study and analyze DNA and protein sequences. It uses a simple text-based format to present sequences and allows for the naming of sequences and inclusion of comments. FASTA is a rapid program that can be used locally or through email servers to find regional similarities between sequences and identify potential matches while ignoring complete sensitivity. It has become a standard tool in biology for sequencing and analyzing proteins and DNA.

1. FASTA
Fatima Khaliq
ROLL #1038
BS(HONS) BOTANY 3rd (M)
University of Education Lahore,
Okara campus, Renalakhurd

2. Table of Contents
 Introduction
 Features of FASTA
 Uses of FASTA
 Data Structure
 Conclusion
 Future Directions
 References

3. Introduction
 Bioformatics is the inter-disciplinary branch of
biology which merges computer science,
mathematics and engineering to study the
biological data.
 FASTA is one of the software which are used by
the biologist to study DNA and protein sequence
either nucleotide or peptide sequence.

4.  This software was originally developed in 1985 by
Lipman and Pearson. Now the 35 version of the
software is available in the market and it is
compatible for MS-Windows, UNIX, Linux and
Mac.
 FASTA provide a text format in which protein
alignment is presented by using single letter
codes. It is also known as FASTA format.

5.  FASTA format allows the sequence naming and
comments to introduce the sequences. The use
of FASTA format has become a standard for
biologist to analyze the sequencing.
 The format of FASTA codes is no longer than 120
characters..

6. Features of FASTA
 Rather than trying to find out the best alignment
between your data, it finds the patches of
regional similarity.
 It is rapid program. You can run the program
locally or you can also send queries to an email
server.

7.  The alignments of FASTA can contain gaps. The
sequence which contain the gap FASTA highlight
those codes with red color.
 Another feature of FASTA is that it ignores the
complete sensitivity and provide information
about the expected matched alignments.

8. USES of FASTA
 FASTA can be use for the alignment of all types
proteins and DNA.
 It can also use for the translation of algorithms
which handle frame shift errors.
 It can used for calculating the similarity which
can help the biologists to decide whether the
alignment is occurred by chance or it is due to
infer homology.

9.  You can also use FASTA for calculating the
optimal score for alignment.
 It can also be used for inferring the functional
and evolutionary relation between sequence can
also help to identify the members of gene family.

10. Data Structure
 Data in FASTA is presented in a single code
sequences. It has got a different search methods
which help in sequencing the proteins. For
example with Smith-waterman type of algorithm
FASTA help you to find out the potential matches
and save your time as well.

11.  While the results of FASTA are reported
in the form of histogram where the
expected values are compared to random
search set. While the lower part of the
histogram contain information about the
matches of interest.

12. Conclusion
 FASTA has become a standard software for the
biologist to analyze and sequencing the proteins
and DNA. Thus, it is one of the easiest software
to not only help them to understand the nature
of sequences but it also allow the biologist to
precede the commenting as well.

13. Future Directions
 Future of FASTA is no doubt very bright as the
advancement in this software are enabling
FASTA to overcome all the limitations which was
present in the previous versions.
 It is also expected that more formats will be
introduced in the future to understand the input
and output of sequencing.

14. Reference
 http://link.springer.com/protocol/10.13
85%2F0-89603-276-0%3A365#page-
1
 http://emboss.sourceforge.net/docs/th
emes/SequenceFormats.html#fut
 http://www.ncbi.nlm.nih.gov/blast/blast
cgihelp.shtml
 http://en.wikipedia.org/wiki/FASTA

15.  http://arep.med.harvard.edu/seqanal/f
asta.html