Detecting overlapping coding sequences in virus genomes
Detecting overlapping coding sequences in virus genomes
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DOI：
10.1186/1471-2105-7-75
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发表时间：
2006-02-16
影响因子：
3
通讯作者：
Brown, CM
中科院分区：
文献类型：
--
作者：
Firth, AE;Brown, CM
背景：检测病毒基因组中的新编码序列（CDS）可能很困难，原因有几个。典型的紧凑型基因组通常包含许多重叠的编码和非编码功能元件，这可能导致不寻常的密码子使用模式;相关序列之间的保守性可能难以解释-特别是在重叠基因内;并且病毒经常采用非规范的翻译机制-例如移码，终止密码子通读，漏扫描和内部核糖体进入位点--这些位点可以隐藏潜在的编码开放阅读框架（ORF）。在以前的论文中，我们介绍了一种新的算法-MLOGD（最大似然重叠基因检测器）-用于检测和分析重叠CDS。在这里，我们提出（a）一个改进的MLOGD统计，（B）一个大大扩展套件的软件使用MLOGD，（c）640病毒序列比对结果的数据库，和（d）的软件和数据库的网络接口。测试表明，从仅20个突变的比对中，MLOGD可以以高达98%的典型准确度区分非重叠CDS和非编码ORF，并且可以以90%的典型准确度检测与已知CDS重叠的CDS。此外，该软件产生了各种统计和图形，有用的分析输入多序列alignment.Conclusion：MLOGD是一个易于使用的工具，用于病毒基因组注释，检测新的CDSs，特别是重叠或短的CDSs，并用于分析重叠的CDSs以下移码位点。该软件、网络服务器、数据库和补充材料可在http://guinevere.otago.ac.nz/mlogd.html上查阅。
Background: Detecting new coding sequences (CDSs) in viral genomes can be difficult for several reasons. The typically compact genomes often contain a number of overlapping coding and non-coding functional elements, which can result in unusual patterns of codon usage; conservation between related sequences can be difficult to interpret-especially within overlapping genes; and viruses often employ non-canonical translational mechanisms-e.g. frameshifting, stop codon readthrough, leaky-scanning and internal ribosome entry sites-which can conceal potentially coding open reading frames (ORFs).Results: In a previous paper we introduced a new statistic-MLOGD (Maximum Likelihood Overlapping Gene Detector)-for detecting and analysing overlapping CDSs. Here we present (a) an improved MLOGD statistic, (b) a greatly extended suite of software using MLOGD, (c) a database of results for 640 virus sequence alignments, and (d) a web-interface to the software and database. Tests show that, from an alignment with just 20 mutations, MLOGD can discriminate non-overlapping CDSs from non-coding ORFs with a typical accuracy of up to 98%, and can detect CDSs overlapping known CDSs with a typical accuracy of 90%. In addition, the software produces a variety of statistics and graphics, useful for analysing an input multiple sequence alignment.Conclusion: MLOGD is an easy-to-use tool for virus genome annotation, detecting new CDSs in particular overlapping or short CDSs-and for analysing overlapping CDSs following frameshift sites. The software, web-server, database and supplementary material are available at http://guinevere.otago.ac.nz/mlogd.html.