Dear Robin,
In a Perl script, you could read your sequences using BioPerl Seq::IO,
create input files, and execute the EMBOSS commands from Perl with
system() or `...`. Remember to close temporary files you've created in
Perl before using them - this forces the last bit of the file to be
really written, rather than stay languishing in some buffer.
This is just one suggestion - there will be other ways. An excellent
guide to Perl is at: http://korflab.ucdavis.edu/Unix_and_Perl
If I remember, some earlier version of needle had a bug which could
affect scores. So you might want to upgrade.
For coding sequences, consider doing the alignment at the protein level
- unless there's a good reason not to. I.e. translate your coding
sequences (perhaps with EMBOSS transeq) and align the translations.
Generally, this will be more sensitive and less easily misled. If you
require nucleotide alignment, you can convert back to the original
nucleotides afterwards - but this is more likely to be required with
multiple alignment than with pairwise (and for multiple alignments can
be achieved with EMBOSS tranalign).
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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