Remark about gap penalties

Peter Rice peter.rice at
Fri Jul 26 15:08:53 UTC 2002

Guy Bottu wrote:
> I just noted something. Some EMBOSS programs (needle, water,...) use a gap
> penalty of type (<gap opening penalty> + (n - 1) * <gap extension penalty>),
> while others (stretcher, matcher,...) use one of type (<gap penalty> + n *
> <gap extension penalty>).

> The "align" libraries of EMBOSS, as far as I
> understand, do not print the score computed by the algorithm but recompute
> the score

Scores are set by the application, through the ajAlignSetScore functions.

The gap penalties are passesd by the application and reported.

The align functions store these as strings so they can be set as integer on
float by the applications.

> Another remark : alignment programs write out a "help" text with line
>   [-outfile]           align      (no help text) align value
> Seems the standard message for "align" is missing.

HELPALIGN and HELPREPORT (and DEFALIGN and DEFREPORT) are missing in the
file emboss/acd/codes.english

You can add these lines to the installed copy of the file:

DEFALIGN     "Write output alignment to"
DEFREPORT    "Write output report to"

HELPALIGN     "Output alignment file name"
HELPREPORT    "Output report file name"



Peter Rice, LION Bioscience Ltd, Cambridge, UK
peter.rice at +44 1223 224723

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