[EMBOSS] Gap cost restrictions for needle/water/stretcher?

Frank Förster frank.foerster at biozentrum.uni-wuerzburg.de
Mon Aug 24 09:01:49 UTC 2009


I have only one question about the allowed gap costs in several programs. I 
using needle, water and stretcher for example.

There are some restrictions to the gap costs a have to use:

1) needle: float from 0-100 for gapopen and 0-10 for gapextend
2) water: float from 0.000-10.000 for gapopen and 0.000-10.000 for gapextend
2) stretcher: positive integer

What are the meaning of these restrictions? I think you use an integer value for 
stretcher (I did not check the source code) and floats for needle/water.

But why the restriction for water to three decimal places?

But more interessting, why the restriction to 0-100/0-10 for needle/water?

Thank you for your efforts!

Frank Förster

Dipl. Biochem. Frank Förster
Department of Bioinformatics
University of Würzburg, Germany
Fon: +49 931 - 318 4555
Fax: +49 931 - 318 4552
frank.foerster at biozentrum.uni-wuerzburg.de

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