罗斯：生成序列家族。

Rose: generating sequence families.

作者信息

Stoye J, Evers D, Meyer F

机构信息

Research Center for Interdisciplinary Studies on Structure Formation (FSPM), University of Bielefeld, Postfach, Germany.

出版信息

Bioinformatics. 1998;14(2):157-63. doi: 10.1093/bioinformatics/14.2.157.

DOI:10.1093/bioinformatics/14.2.157

PMID:9545448

Abstract

MOTIVATION

We present a new probabilistic model of the evolution of RNA-, DNA-, or protein-like sequences and a software tool, Rose, that implements this model. Guided by an evolutionary tree, a family of related sequences is created from a common ancestor sequence by insertion, deletion and substitution of characters. During this artificial evolutionary process, the 'true' history is logged and the 'correct' multiple sequence alignment is created simultaneously. The model also allows for varying rates of mutation within the sequences, making it possible to establish so-called sequence motifs.

RESULTS

The data created by Rose are suitable for the evaluation of methods in multiple sequence alignment computation and the prediction of phylogenetic relationships. It can also be useful when teaching courses in or developing models of sequence evolution and in the study of evolutionary processes.

AVAILABILITY

Rose is available on the Bielefeld Bioinformatics WebServer under the following URL: http://bibiserv.TechFak.Uni-Bielefeld.DE/rose/ The source code is available upon request.

CONTACT

folker@TechFak.Uni-Bielefeld.DE

摘要

动机

我们提出了一种新的RNA、DNA或蛋白质类序列进化的概率模型以及一个实现该模型的软件工具Rose。在进化树的引导下，通过字符的插入、删除和替换，从一个共同祖先序列创建出一组相关序列。在这个人工进化过程中，记录“真实”历史并同时创建“正确”的多序列比对。该模型还允许序列内的突变率变化，从而能够建立所谓的序列基序。