Dear Henrikki,
You could use the bl2seq program from the BLAST suite. It does always
try both strands of the second sequence. If you need to have it under
EMBOSS, you could use the wrappers4EMBOSS suite
(http://wemboss.sourceforge.net). Note by the way that stretcher makes a
global alignment, for a local alignment you would have to use matcher.
Regards,
Guy Bottu,
Belgian EMBnet Node
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