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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?

https://www.rcsb.org/fasta/entry/6EQJ

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.

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  • $\begingroup$ Why would gene synthesis require ascii format? $\endgroup$
    – user40950
    Jul 31, 2020 at 20:53
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    $\begingroup$ What do you mean with ascii? FASTA is plain text. $\endgroup$
    – Chris ♦
    Jul 31, 2020 at 21:30

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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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