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16.1: Introduction

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FASTA Format

Biological sequences are passed to software in a standardized format referred to as FASTA. FASTA is a plain text format that can be read in any text editor (TextEdit, Notepad, VIM, TextWrangler, etc.). Nucleic acids (DNA and RNA) and Proteins are represented by single-letter nucleotides (A, T, C, G) or single letter amino acid (20 amino acids). FASTA sequences begin with a > character in the first line followed by some descriptive information about the sequence, like a sequence name. The next line consists of the sequence information. A FASTA file can contain multiple sequence entries all demarcated by a new line and a title line beginning with >.


Example FASTA File

> Made-up nucleic acid sequence
ATATAGGGATTAGGATTAGAGGATAGAGGGGATTGCGCCG
> Another nucleic acid sequence in the same file
GGGTCGGGCTAGCGGAATCGGATTCGGCATTCGGATATTCGGATTCGGAT


FASTA files are plain text but usually have an extension indicating it as a sequence file: .fasta, .fa, .fna or even .txt

A list of single-letter codes for nucleic acids follows below:

Nucleic Acid Code Meaning Mnemonic
A A Adenine
C C Cytosine
G G Guanine
T T Thymine
U U Uracil
R A or G puRine
Y C, T, or U pYrimidines
K G, T, or U bases which are Ketones
M A or C bases with aMino groups
S C or G Strong interaction
W A, T, or U Weak interaction
B not A (i.e. C, G, T, or U) B comes after A
D not C (i.e. A, G, T, or U) D comes after C
H not G (i.e., A, C, T, or U) H comes after G
V neither T nor U (i.e. A, C, or G) V comes after U
N A, C, G, T, U Nucleotide
X masked
Gap of indeterminate length

Graphical Sequence Manipulation

The exercises described here regarding bioinformatics will utilize a free and open-source software called Unipro UGENE.


This page titled 16.1: Introduction is shared under a CC BY-NC-SA 4.0 license and was authored, remixed, and/or curated by Bio-OER.

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