[bip] FASTA

[Erich Schwarz]

On Wed, 1 Aug 2007, Bruce Southey wrote:

> This type of reaction is rather surprising given that original
> source of the format allows OPTIONAL comment lines starting with
> ';'.  The arguments that the 'file format has evolved' or there is
> some standard are incorrect because it appears to be have been
> present from the beginning.

    The arguments may be "incorrect" in the sense that, if one goes
back to Pearson's original definition of the FASTA format in the
mid-1980s, one can find comment lines with leading ";" characters.
However, even if the arguments are "incorrect", they're *true*
because they're actually describing how the vast amount of existing
code designed to handle FASTA formats is designed to run, in 2007
A.D.

    It may be good or bad that NCBI's version of FASTA format became
the de facto (as opposed to de jure) standard, but that it *has*
done so strikes me as rather glaringly plain.


--Erich