[Bioperl-l] Changes in FASTA output format

David Messina dmessina at wustl.edu
Fri Mar 30 16:24:26 EDT 2007

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

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