PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database
PRIMROSE: a computer program for generating and estimating the phylogenetic range of 16S rRNA oligonucleotide probes and primers in conjunction with the RDP-II database
复制标题
DOI：
10.1093/nar/gkf450
复制
发表时间：
2002-08-01
影响因子：
14.9
通讯作者：
Fry, JC
中科院分区：
文献类型：
--
作者：
Ashelford, KE;Weightman, AJ;Fry, JC
我们描述了报春花，用于识别16 S rRNa探针和PCR引物的计算机程序，用作细菌鉴定和计数中的系统发育和生态工具。报春花旨在使用核糖体数据库项目（RDP）的数据来寻找具有多达两个简并位置的潜在有用的寡核苷酸。然后可以探索这些和其他现有寡核苷酸的分类范围，从而快速鉴定合适的寡核苷酸。报春花包括允许使用用户定义的序列数据库的功能。使用RDP数据库的程序的计算机模拟试验鉴定了描述其靶分类群的寡核苷酸，其准确度远远高于目前使用的等同寡核苷酸。我们确定了寡核苷酸的变形菌的亚类和噬细胞杆菌-拟杆菌（CFB）司。这些寡核苷酸描述了高达94.7%的目标分类单元，非目标命中少于50个，作者建议进一步研究它们。与ARB软件包中的PROBE DESIGN比较表明，报春花能够以更高的特异性识别寡核苷酸。报春花具有直观的图形用户界面，可在Microsoft Windows 95/NT/2000操作系统上运行。它是开源的，可以从作者那里免费获得。
We describe PRIMROSE, a computer program for identifying 16S rRNa probes and PCR primers for use as phylogenetic and ecological tools in the identification and enumeration of bacteria. PRIMROSE is designed to use data from the Ribosomal Database Project (RDP) to find potentially useful oligonucleotides with up to two degenerate positions. The taxonomic range of these, and other existing oligonucleotides, can then be explored, allowing for the rapid identification of suitable oligonucleotides. PRIMROSE includes features to allow user-defined sequence databases to be used. An in silico trial of the program using the RDP database identified oligonucleotides that described their target taxa with a degree of accuracy far greater than that of equivalent currently used oligonucleotides. We identify oligonucleotides for subdivisions of the Proteobacteria and for the Cytophaga-Flexibacter-Bacteroides (CFB) division. These oligonucleotides describe up to 94.7% of their target taxon with fewer than 50 non-target hits, and the authors recommend that they be investigated further. A comparison with PROBE DESIGN within the ARB software package shows that PRIMROSE is capable of identifying oligonucleotides with a higher specificity. PRIMROSE has an intuitive graphical user interface and runs on the Microsoft Windows 95/NT/2000 operating systems. It is open source and is freely available from the authors.