Sequence Database Search Using Jumping Alignments
Rainer Spang, Marc Rehmsmeier and Jens Stoye
August 2000
We describe a new algorithm for amino acid sequence classification
and the detection of remote homologues. The algorithm is based on the
dynamic programming principle and evaluates the fit of a candidate sequence
to a given family of sequences by means of a new score called the ``jumping
alignment score''. In a jumping alignment, a candidate sequence is locally
aligned to one reference sequence in the family, and in addition
the reference sequence may change within the alignment.
We show that the algorithm performs well in recovering subfamilies of the SCOP database.
Keywords: homology search, dynamic programming, bioinformatics
The manuscript is available in postscript format