[Bioperl-l] Changes in FASTA output format

[David Messina]

> I could even imagine tagging the lines:
>
>   Algorithm:  Smith-Waterman (SSE2, Michael Farrar 2006) (6.0 Mar  
> 2007)
>   Parameters:  BL50 matrix (15:-5), open/ext: -12/-2
> Scan time:  2.140

IMO, tagged lines would be great and make parsing very easy.


> (2)  I am also thinking about displaying multiple E()-values,
> depending on whether they are calculated from the similarity search
> or the shuffled high scores, e.g., going from:
>
> [...]
>
> I think this output would break many more FASTA parsers, and one
> option would be (initially) to add it only to the alignment output.

Agreed, but...


> Naturally, initially it will be easy to revert to the classic format.

I think the backwards compatibility you describe here would take care  
of those cases.


My two cents (and thanks for asking :),
Dave

--
Dave Messina
Senior Analyst, Assembly Group
Genome Sequencing Center
Washington University
St. Louis, MO