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Title: Biological Significance of Jumping Alignments
P12
Bannert, Constantin; Stoye, Jens

bannert@techfak.uni-bielefeld.de
Bielefeld University, Germany

In the absence of 3D structure, the classification of a protein domain into a given familiy of homologous sequences has to rely on the exploitation of sequence information alone. A multiple alignment of the family is the basis for most classification methods. Traditional methods use either row-based (horizontal) or column-based (vertical) information from the multiple alignment in this classification process.

The recently proposed jumping alignment algorithm tries to improve sensitivity and specificity by using a combination of both horizontal and vertical information. At each site of the multiple alignment the query is aligned to one sequence of the protein family. Between sites, the reference sequence may change while each such 'jump' is penalized. So far it has not been examined if and to what extent these jumps represent biological signals.

We present first results on the structural and functional significance of jumps in the jumping alignment context. We expect that the results can be used to further improve the detection of remote(ly)! homologous amino acid sequences by incorporating structural information from the protein family.