Andrea,
Most tools use blast or other local alignment search algorithms to do
the initial searching, and then use a global alignment algorithm to
align the hits. For example DbClustal
http://igbmc.u-strasbg.fr:8080/DbClustal/Documentation/what.html which
uses blastp to identify the hits, and then uses Clustal to align them
. If you search with an hmm model (using hmmsearch) that would be a
global search, but that only works on protein sequences. I guess it's
possible to use needle or stretcher from EMBOSS
http://www.hgmp.mrc.ac.uk/Software/EMBOSS/Apps/alignment_global_group.html
and make an
individual alignment to all sequences in a database, and then sort
according to best score.
Stefanie
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