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内蒙古自治区呼和浩特市赛罕区大学西街235号 邮编: 010021
作者机构:Osaka Univ Grad Sch Engn Sci Toyonaka Osaka 5608531 Japan
出 版 物:《IEICE TRANSACTIONS ON FUNDAMENTALS OF ELECTRONICS COMMUNICATIONS AND COMPUTER SCIENCES》 (电子信息通信学会汇刊:电子学、通信及计算机科学基础)
年 卷 期:2000年第E83A卷第4期
页 面:713-721页
核心收录:
学科分类:0808[工学-电气工程] 0809[工学-电子科学与技术(可授工学、理学学位)] 08[工学] 0812[工学-计算机科学与技术(可授工学、理学学位)]
主 题:maximum-density subgraph approximate string comparison maximum flow algorithm protein sequence analysis computational molecular biology
摘 要:In this paper, we propose a method for detecting conserved domains from a set of amino acid sequences that belong to a protein family. This method detects the domains as follows: first, generate fixed-length subsequences from the sequences;second, construct a weighted graph that connects any two of the subsequences (vertices) having higher similarity than a pre-defined threshold;third, search for the maximum-density subgraph for each connected component of the graph;finally, explore conserved domains in the sequences by combining the results of the previous step. From the performance results obtained by applying the method to several protein families that have complex conserved domains, we found that our method was able to detect those domains even though some domains were weakly conserved.