[Bioperl-l] Changes in FASTA output format
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
> 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.
> 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 :),
Senior Analyst, Assembly Group
Genome Sequencing Center
St. Louis, MO
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