Incremental generation of summarized clustering hierarchy for protein family analysis
Resource
Bioinformatics 20 (16): 2586-2596
Journal
Bioinformatics
Journal Volume
20
Journal Issue
16
Pages
2586-2596
Date Issued
2004
Date
2004
Author(s)
Abstract
MOTIVATION: Protein sequence clustering has been widely exploited to facilitate in-depth analysis of protein functions and families. For some applications of protein sequence clustering, it is highly desirable that a hierarchical structure, also referred to as dendrogram, which shows how proteins are clustered at various levels, is generated. However, as the sizes of contemporary protein databases continue to grow at rapid rates, it is of great interest to develop some summarization mechanisms so that the users can browse the dendrogram and/or search for the desired information more effectively. RESULTS: In this paper, the design of a novel incremental clustering algorithm aimed at generating summarized dendrograms for analysis of protein databases is described. The proposed incremental clustering algorithm employs a statistics-based model to summarize the distributions of the similarity scores among the proteins in the database and to control formation of clusters. Experimental results reveal that, due to the summarization mechanism incorporated, the proposed incremental clustering algorithm offers the users highly concise dendrograms for analysis of protein clusters with biological significance. Another distinction of the proposed algorithm is its incremental nature. As the sizes of the contemporary protein databases continue to grow at fast rates, due to the concern of efficiency, it is desirable that cluster analysis of a protein database can be carried out incrementally, when the protein database is updated. Experimental results with the Swiss-Prot protein database reveal that the time complexity for carrying out incremental clustering with k new proteins added into the database containing n proteins is O(n2betalogn), where beta congruent with 0.865, provided that k << n. AVAILABILITY: The Linux executable is available on the following supplementary page.
Type
journal article
File(s)![Thumbnail Image]()
Loading...
Name
13.pdf
Size
134.13 KB
Format
Adobe PDF
Checksum
(MD5):a62324afabd7d7f441ad883d68d10eb0