FASTA format - proposed max line limit

Andrew Dalke dalke at bioreason.com
Mon Dec 7 11:21:56 EST 1998


Jerry Learn <learn at u.washington.edu> said:
> I'm glad I provided you with an opportunity to tell us all about
> MIME and email. 

  I apologize.  I had a tendency to write email that's too
tutorial-like.  I meant no slur on your or anyone else's knowledge
of email.


  The point of my response was to say that the criterion for
a file format should not be determined by the limitations of
non-MIME based email.  In addition to the display problems
presented by some email clients there are hidden dangers present
in standard email.  One of them is the ">From" issue I pointed out.
These are not well known but have consequences on sending files as
raw email text.  There may be other considerations I don't know
about, esp. as regards non-unix mailers.

> If they want to name their sequences using "From yeast" and
> "From E. coli," then I ahve to hav a different discussion on
> how to name one's sequences.

  That choice of names was for example purposes only.  There's 
no reason that something similar isn't going to happen.  For example,
consider a program that merges multiple sequence records as the
following:

 >sp|0001
 AAAA
 >gb|0002 
 AAAA
 >sp|0009

merged into
 >From sp|0001, gb|0002 and sp|0009
 AAAA

In this case the author decided to make the comments of the merged
record more human readable.

						Andrew Dalke
						dalke at bioreason.com




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