Is there an algorithm or tool to convert a fasta sequence file (such as the file linked below) into an ascii file for the purpose of gene synthesis?


To the best of my knowledge, the fasta file contains the entire sequence of a protein, in which case there must be a way to convert it to a standard ascii formatted sequence, but I havent been able to find any tools to do so.

  • $\begingroup$ Why would gene synthesis require ascii format? $\endgroup$
    – Cell
    Jul 31 '20 at 20:53
  • 2
    $\begingroup$ What do you mean with ascii? FASTA is plain text. $\endgroup$
    – Chris
    Jul 31 '20 at 21:30

FASTA files are just text files, so you can open them up in your favorite text editor to see what they look like. The file you linked has a single entry. The first line begins with > and contains information about the sequence, delimited by | characters – the accession number, chain info, gene name, species, etc. Subsequent lines are just the protein sequence using the standard 20-letter alphabet for amino acids, or the nucleotide sequence from 5'-3' using ACTG. There can be multiple entries in a file, delineated by one or more blank lines.

If for whatever reason your instrument or vendor won't accept FASTA files, a very simple low-throughput solution is to just delete the first line of single-entry files, or delete any lines beginning with > for multiple-entry files. If you have many files to process, this can be automated using Unix/Linux command line tools or a scripting language like Python or Perl.


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