NDLI: Synthesizing Aligned Random Pattern Digraphs from protein sequence patterns

Content Provider	IEEE Xplore Digital Library
Author	Lee, A.E. Wong, A.K.C.
Copyright Year	2011
Description	Author affiliation: Systems Design Engineering, University of Waterloo, Waterloo, Canada (Lee, A.E.; Wong, A.K.C.)
Abstract	An essential step of protein function analysis is to discover patterns that represent functional regions in a set of protein family sequences. However, the same functional region of a protein family that occurs in different sequences may contain variations that resulted from biological substitutions, deletions, and insertions. Thus, a sequence pattern representing this functional region seldom repeats precisely at the exact position with the same amino acid residues. To capture these variable associations, we developed a pattern synthesis process. First, we used an effective sequence pattern discovery algorithm to discover high order patterns as input. Next, we group and align these similar discovered patterns into Aligned Random Pattern Clusters (ARPCs). During the clustering process, each ARPC is transformed into a probabilistic structural pattern called the Aligned Random Pattern Digraph (ARPD). The advantages of our synthesis process are 1) the synthesized patterns are not confined to a fixed protein region since the ARPCs captures the similar patterns by their variable sites, 2) the ARPDs retain both horizontal pattern associations and vertical site variations, and 3) the search space for synthesizing input patterns is smaller than that for aligning input sequences. Our method successfully discovers two functional protein regions of the Cytochrome Complex protein family: the proximal and distal binding segment that binds the iron molecule of the heme ligand from each side of the plane without relying on prior knowledge.
Starting Page	178
Ending Page	185
File Size	1189478
Page Count	8
File Format	PDF
ISBN	9781457716126
e-ISBN	9781457716133
DOI	10.1109/BIBMW.2011.6112372
Language	English
Publisher	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Publisher Date	2011-11-12
Publisher Place	USA
Access Restriction	Subscribed
Rights Holder	Institute of Electrical and Electronics Engineers, Inc. (IEEE)
Subject Keyword	Proteins Protein engineering Pattern Runtime Hidden Markov models Protein Function Prediction Probabilistic logic Iron Aligned Random Pattern Digraph Indexes Clustering
Content Type	Text
Resource Type	Article

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