[EMBOSS] Needle with penalty for end gaps

Frank Förster Frank.Foerster at biozentrum.uni-wuerzburg.de
Tue Aug 18 18:15:44 UTC 2009


in the announcement-thread  of the new EMBOSS version 6.1.0. was a
request for a program allowing complete global alignments including
penalties for end gaps by Daniel Barker. (
http://www.mail-archive.com/emboss@lists.open-bio.org/msg01202.html )

The suggestion was to add a command line parameter to the needle program
to enable/disable the penalties.

Are there any news on this topic? I have to perform a lot of pairwise
global alignments (without free end gaps) and either I have to program
my own software or use existing software. Needle owns all needed
features except the "only free end behavior". So I am really interested
in getting a version of needle able to help me ;)

Thanks for the great EMBOSS package.


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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