pHMM-tree: phylogeny of profile hidden Markov models

被引:15
作者
Huo, Luyang [1 ]
Zhang, Han [1 ]
Huo, Xueting [1 ]
Yang, Yasong [2 ]
Li, Xueqiong [2 ]
Yin, Yanbin [2 ]
机构
[1] Nankai Univ, Coll Comp & Control Engn, Tianjin, Peoples R China
[2] Northern Illinois Univ, Dept Biol Sci, De Kalb, IL 60115 USA
基金
美国国家卫生研究院;
关键词
DATABASE;
D O I
10.1093/bioinformatics/btw779
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Protein families are often represented by profile hidden Markov models (pHMMs). Homology between two distant protein families can be determined by comparing the pHMMs. Here we explored the idea of building a phylogeny of protein families using the distance matrix of their pHMMs. We developed a new software and web server (pHMM-tree) to allow four major types of inputs: (i) multiple pHMM files, (ii) multiple aligned protein sequence files, (iii) mixture of pHMM and aligned sequence files and (iv) unaligned protein sequences in a single file. The output will be a pHMM phylogeny of different protein families delineating their relationships. We have applied pHMM-tree to build phylogenies for CAZyme (carbohydrate active enzyme) classes and Pfam clans, which attested its usefulness in the phylogenetic representation of the evolutionary relationship among distant protein families.
引用
收藏
页码:1093 / 1095
页数:3
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