13 0

A novel specialized single-linkage clustering algorithm for taxonomically ordered data

Title
A novel specialized single-linkage clustering algorithm for taxonomically ordered data
Author
Klaus Heese
Keywords
BURROWS-WHEELER TRANSFORM; READ ALIGNMENT; SEQUENCES; GENE
Issue Date
2017-06
Publisher
ACADEMIC PRESS LTD- ELSEVIER SCIENCE LTD
Citation
JOURNAL OF THEORETICAL BIOLOGY, v. 427, page. 1-7
Abstract
Similarities among ortholog genes for a given set of species S can be expressed by alignment matrices, where each matrix cell results from aligning a gene transcript against the genome of a species within S. Gene clusters can be computed by using single-linkage clustering in time n x m, where n denotes the number of ortholog genes and m denotes the number of inspected assemblies. Our approach can break the 0(n x m) complexity of single-linkage clustering by exploiting an order among species that results from an in-order traversal of a given phylogenetic tree. The order among species allows the reduction of the inspected scope of the matrix to taxonomically related combinations of assemblies and genes, thus lowering the computational efforts necessary for creating the alignment matrix without affecting cluster quality. We present two novel approaches for clustering. First, we introduce a hierarchical clustering with, omitting the initial sorting of ISM elements, amortized O(|S|) time behavior, where it holds |S| <= n + m. Then, we propose a consecutive clustering having a linear time complexity O(|S|). Both approaches compute identical clusters, whereas dendrograms can only be obtained from the hierarchical one. We prove that our approaches deliver higher cluster densities than single linkage clustering. Additionally, we show that we compute clusters of superior quality, which ensures that our approaches are generally less error prone. (C) 2017 Elsevier Ltd. All rights reserved.
URI
https://www.sciencedirect.com/science/article/pii/S0022519317302163?via%3Dihubhttp://repository.hanyang.ac.kr/handle/20.500.11754/114521
ISSN
0022-5193; 1095-8541
DOI
10.1016/j.jtbi.2017.05.008
Appears in Collections:
GRADUATE SCHOOL OF BIOMEDICAL SCIENCE AND ENGINEERING[S](의생명공학전문대학원) > ETC
Files in This Item:
There are no files associated with this item.
Export
RIS (EndNote)
XLS (Excel)
XML


qrcode

Items in DSpace are protected by copyright, with all rights reserved, unless otherwise indicated.

BROWSE