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Sequence database search using jumping alignments

Spang, Rainer ; Rehmsmeier, M. ; Stoye, J.


We describe a new algorithm for amino acid sequence classification and the detection of remote homologues. The rationale is to exploit both vertical and horizontal information of a multiple alignment in a well balanced manner. This is in contrast to established methods like profiles and hidden Markov models which focus on vertical information as they model the columns of the alignment ...


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