SPEM (Sequence and secondary-structure Profiles Enhanced Multiple alignment) aligns multiple sequences using pre-processed sequence profiles and predicted secondary structures for pairwise alignment, consistency-based scoring for refinement of the pairwise alignment and a progressive algorithm for final multiple alignment.
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Bioinformatics. 2005 Sep 15;21(18):3615-21. Epub 2005 Jul 14.
SPEM: improving multiple sequence alignment with sequence profiles and predicted secondary structures.
Zhou H1, Zhou Y.