[EMBOSS] EMBOSS 6.1.0 release now available

[Daniel Barker]

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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