FASTA format - proposed max line limit

Andrew Dalke dalke at bioreason.com
Sun Dec 6 01:39:05 EST 1998

Jerry Learn <learn at u.washington.edu> commented:
> One other benefit with constraining the comment line to 80 characters is
> that the sequence files are e-mailable. Often I ask collaborators to send
> me sequence data via email. It is usually the most convenient LCD method
> to exchange data. If the comment line is >80 characters, the remaining
> characters become sequence data.

That's why there are MIME attachments.  Most modern mailers (the
formal MIME definition started with RFC 1341 in 1992) let you attach
files to your email.  Many cheap or even free email clients exist
to handle this sort of mail, ranging from Eudora to Netscape to
PINE, ELM and Mutt.  There's no reason to expect that a "least common
denominator" approach cannot take advantage of that.

Even before MIME you could still send uuencoded mail.  In the good old
days I sent lots of mail like:
 cat /etc/passwd | compress | uuencode passwd.Z | Mail dalke at acm.org
(Let's see who tries that out :)

That's how people sent (and still send) images on Usenet.  Most capable
news readers can automatically decode those mailings even when sent
as several posts.  (Sent as several posts because another limitation
of mail/usenet is a hard limit by some gateways on message size.
And there's no way a format will get around that limitation.)

Also, do you know what sorts of mangling occur for email to get
to you.  You mentioned forcing line wraps (even though the SMTP
RFC says mailer should allow long lines) but do you know about the
"From " problem?  Take a look at:


The "mbox" mailbox format uses a line that starts "From " to indicate
the start of a new email message.  If text in the body starts with
"From ", the local mail delivery agent (the program that puts the
new email in the file) is supposed to escape the "From " with
">From ".  The mail reader is then supposed to unescape it so
you never see the leading ">".  However, the original format did
not escape escaped test (eg, convert ">From" to ">>From", ">>From"
to ">>>From", etc.)

Quoting from the above url (and with a different quote character :)
| The original mboxo format quotes  only  From_  lines,  not
| >From_  lines.   As  a  result  it  is  impossible to tell
|  whether
|        From: djb at silverton.berkeley.edu (D. J. Bernstein)
|        To: god at heaven.af.mil
|        >From now through August I'll be doing beta  testing.
|        Thanks for your interest.
|  was quoted in the original message.

Before you object, I do get email that is escaped this way;
where I see the additional ">" in the front of mail body lines
starting with "From ".

In fact, let's try it out :)

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