[EMBOSS] fasta single-line sequence format?

Peter Rice ricepeterm at yahoo.co.uk
Tue Aug 27 09:41:13 UTC 2013

On 27/08/2013 09:40, Niels Larsen wrote:
> EMBOSS list,
> I could not find a fasta single-line sequence format, is it
> missing? having the sequence as a single line does not
> violate fasta format i think, and many programs use it
> because of speed and indexing convenience.

You mean as an output format I assume? (it would be no problem for input).

Easy to implement, but needs a name so you can so specify
-osformat fastasingle (for example)

It can also be an issue for applications that fail to check for very 
long input lines.

I don't see any real benefit for indexing - you only need to point to 
the start of the ID line for that. Maybe there are applications that map 
the sequence string and want to have no extra characters.


Peter Rice

More information about the EMBOSS mailing list