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 :
No SC013532
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