[EMBOSS] EMBOSS 6.1.0 release now available
Daniel Barker
db60 at st-andrews.ac.uk
Wed Jul 15 12:47:17 UTC 2009
Dear Alan,
Very glad to see the project will continue with new funding.
One request. Could EMBOSS please add a full global alignment program or
option? Needle allows 'overhanging ends' with no penalty. From the
current Needle documentation: 'There is no penalty for the hanging ends
of the overlap. In bioinformatics, it is usually reasonable to assume
that the sequences are incomplete and there should be no penalty for
failing to align the missing bases.'
For protein alignments, this tends to be very lenient towards alignments
with these kinds of domain architecture:
protein 1: A-B-C
protein 2: C-X-Y-Z
As opposed to the following situation, which (correctly for global
alignment) does tend to be heavily penalized:
protein 1: A-C-D
protein 2: C
I don't think this makes sense. Or at least, it definitely does not make
sense for all applications. Generally with pairwise alignment of
proteins I want either local alignment (e.g. water), or full global
alignment which isn't available in EMBOSS.
Thank you for considering this.
Best regards,
Daniel
--
Daniel Barker
http://bio.st-andrews.ac.uk/staff/db60.htm
The University of St Andrews is a charity registered in Scotland :
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