How to Convert Sequence to Fasta

One common goal in medical research involves identification of errors, or mutations, in DNA sequence that could cause genetic related disease. Technology and computer science have advanced genetic research to a level where thousands of sequence data can be analyzed simultaneously. One stipulation of newer software is prior conversion of sequence data into FASTA format. FASTA is similar to simple text format. It allows multiple pieces of data to be compiled into a single file and accelerates analysis. However, most instruments generate sequence files in text format. Converting text to FASTA format is a simple process using text editor software.

Things You'll Need

• Computer
• Text editor program

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Instructions

• 1

  Open the designated DNA sequence text file using text-editing program. This would be Text Editor for MacIntosh and Note Pad for Windows compatible systems. Original sequence text files could have an alternative extension such as seq for data generated on an Applied Biosystems automated genetic analyzer.

• 2

  Begin the first line by typing > followed by a sequence identifier. The greater than symbol designates FASTA format for programs that analyze FASTA data. There are no specific rules concerning the identifier as long as there are no spaces. An example of an acceptable entry for the first line is >Cat_Isomerase_Exon3.

• 3

  Press the "Return" key to create a line break and begin the second line.

• 4

  Begin sequence data on line two. FASTA format guidelines require DNA text data following International Union of Pure and Applied Chemistry, IUPAC, codes. Each line is limited to 80 characters representing 80 DNA bases and can be upper or lower case. An acceptable entry including mixed bases is AGCTTCGTGG...CVTGCGTTGT.

• 5

  Press the "Return" key to begin the next line of sequence data. Each line should consist of 80 bases represented by the IUPAC code.

• 6

  Save the file using the txt file extension or appropriate FASTA file extension. Programs that process FASTA formatted data often require a FASTA specific extension such as fsa, fna, ffn or frn.