Paper Info
Title
Modified PrefixSpan Method for Motif Discovery in Sequence Databases
Abstract
We propose a motif discovery system that uses a modified PrefixSpan method to extract frequent patterns from an annotated sequence database that has such attributes as a sequence identifier (sequence-id), a sequence, and a set of items. The annotations are represented as the set of items in the database. Frequent sequence patterns and frequent item patterns are extracted from the annotated sequence database. Frequent sequence patterns are located in both identical and non-identical positions among those sequences. In general, the existing PrefixSpan method can extract a large number of identical patterns from the sequence databases. However, the method does not include a function to extract frequent patterns together with gaps or wild character symbols. This new method allows the incorporation of gap characters. Moreover, the method allows effective handling of the annotated sequence database that consists of a set of tuples including a sequence together with a set of items. Furthermore, the prototype has been applied to the evaluation of three sets of sequences that include the Zinc Finger, Cytochrome C, and Kringle motifs.
Year
DOI
Venue
2002
10.1007/3-540-45683-X_52
PRICAI
Keywords
Field
DocType
motif discovery,sequence databases,sequence identifier,existing prefixspan method,annotated sequence database,identical pattern,modified prefixspan method,frequent sequence pattern,new method,frequent pattern,frequent item pattern,zinc finger,cytochrome c
PrefixSpan,Sequence logo,Sequence database,Pattern recognition,Identifier,Computer science,Tuple,Motif (music),Association rule learning,Artificial intelligence,Zinc finger,Database
Conference
ISBN
Citations 
PageRank 
3-540-44038-0
4
0.62
References 
Authors
8
5
Name
Order
Citations
PageRank
H. Kitakami19449.68
Tomoki Kanbara240.62
Yasuma Mori3219.89
Susumu Kuroki42398.05
Yukiko Yamazaki540.62