MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes.
MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes.
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DOI：
10.1093/nar/gki498
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发表时间：
2005-07-01
影响因子：
14.9
通讯作者：
Médigue C
中科院分区：
文献类型：
--
作者：
Cruveiller S;Le Saux J;Vallenet D;Lajus A;Bocs S;Médigue C
新测序的细菌基因组的注释始于运行几种自动分析方法，主要侧重于蛋白质编码基因的识别。DNA序列在局部核苷酸组成上是异质的，这有时导致当它们不是蛋白质编码基因或是真实但未表征的蛋白质编码基因时，序列被注释为真实基因。该第一注释步骤之后通常是预测基因的专家手动注释。随后将以适当的数据库文件格式组织的基因组数据（序列和注释）提交给国际核苷酸序列数据库的入口点。这些过程不可避免地会出现错误，这可能会导致无意中的语法注释错误存储在公共数据库中。在这里，我们提出了一个新的网络程序，MICheck（MICrobial基因组测序），使注释的基因和移码集在以前公布的细菌基因组的快速验证。网络界面允许人们轻松地调查MICheck结果，即不准确或遗漏的基因注释：绘制图形表示，其中使用关于编码潜力（曲线）和相邻基因注释的信息给出独特编码DNA序列注释或预测移码的基因组背景。我们通过对20个细菌基因组的分析来说明MICheck网站的一些功能，其中9个是在国家生物技术信息中心（NCBI）参考序列项目（RefSeq）中选择的“已审查”状态。在微生物基因组的许多重新注释项目的背景下，该工具可以被视为功能重新注释步骤之前的初步步骤，以快速检查缺失或错误注释的基因。MICheck网站可通过以下地址访问：
The annotation of newly sequenced bacterial genomes begins with running several automatic analysis methods, with major emphasis on the identification of protein-coding genes. DNA sequences are heterogeneous in local nucleotide composition and this leads sometimes to sequences being annotated as authentic genes when they are not protein-coding genes or are true but uncharacterized protein-coding genes. This first annotation step is generally followed by an expert manual annotation of the predicted genes. The genomic data (sequence and annotations) organized in an appropriate databank file format is subsequently submitted to an entry point of the International Nucleotide Sequence Database. These procedures are inevitably subject to mistakes, and this can lead to unintentional syntactic annotation errors being stored in public databanks. Here, we present a new web program, MICheck (MIcrobial genome Checker), that enables rapid verification of sets of annotated genes and frameshifts in previously published bacterial genomes. The web interface allows one easily to investigate the MICheck results, i.e. inaccurate or missed gene annotations: a graphical representation is drawn, in which the genomic context of a unique coding DNA sequence annotation or a predicted frameshift is given, using information on the coding potential (curves) and annotation of the neighbouring genes. We illustrate some capabilities of the MICheck site through the analysis of 20 bacterial genomes, 9 of which were selected for their ‘Reviewed’ status in the National Center for Biotechnology Information (NCBI) Reference Sequence Project (RefSeq). In the context of the numerous re-annotation projects for microbial genomes, this tool can be seen as a preliminary step before the functional re-annotation step to check quickly for missing or wrongly annotated genes. The MICheck website is accessible at the following address: .
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影响因子：
3
作者：
Larsen TS;Krogh A
通讯作者：
Krogh A
影响因子：
3
作者：
Bocs S;Danchin A;Médigue C
通讯作者：
Médigue C
影响因子：
7
作者：
Médigue, C;Rose, M;Danchin, A
通讯作者：
Danchin, A
影响因子：
14.9
作者：
Pruitt KD;Tatusova T;Maglott DR
通讯作者：
Maglott DR
影响因子：
14.9
作者：
Mulder, NJ;Apweiler, R;Zdobnov, EM
通讯作者：
Zdobnov, EM