FlaGs 和 webFlaGs：通过基因邻域保守性分析发现新的生物学功能。
FlaGs and webFlaGs: discovering novel biology through the analysis of gene neighbourhood conservation.
机构信息
Department of Molecular Biology and Umeå Centre for Microbial Research, Umeå University, Umeå 901 87, Sweden.
Department of Chemistry, KTH Royal Institute of Technology, Stockholm 100 44, Sweden.
出版信息
Bioinformatics. 2021 Jun 9;37(9):1312-1314. doi: 10.1093/bioinformatics/btaa788.
SUMMARY
Analysis of conservation of gene neighbourhoods over different evolutionary levels is important for understanding operon and gene cluster evolution, and predicting functional associations. Our tool FlaGs (standing for Flanking Genes) takes a list of NCBI protein accessions as input, clusters neighbourhood-encoded proteins into homologous groups using sensitive sequence searching, and outputs a graphical visualization of the gene neighbourhood and its conservation, along with a phylogenetic tree annotated with flanking gene conservation. FlaGs has demonstrated utility for molecular evolutionary analysis, having uncovered a new toxin-antitoxin system in prokaryotes and bacteriophages. The web tool version of FlaGs (webFlaGs) can optionally include a BLASTP search against a reduced RefSeq database to generate an input accession list and analyse neighbourhood conservation within the same run.
AVAILABILITY AND IMPLEMENTATION
FlaGs can be downloaded from https://github.com/GCA-VH-lab/FlaGs or run online at http://www.webflags.se/.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
摘要
分析不同进化水平上基因邻域的保守性对于理解操纵子和基因簇的进化以及预测功能关联非常重要。我们的工具 FlaGs（代表侧翼基因）以 NCBI 蛋白质访问码列表作为输入，使用敏感的序列搜索将邻域编码的蛋白质聚类到同源组中，并输出基因邻域及其保守性的图形可视化，以及带有侧翼基因保守性注释的系统发育树。FlaGs 已被证明在分子进化分析中具有实用性，它在原核生物和噬菌体中发现了一种新的毒素-抗毒素系统。FlaGs 的网络工具版本（webFlaGs）可以选择包括对简化 RefSeq 数据库的 BLASTP 搜索，以生成输入访问码列表，并在同一运行中分析邻域的保守性。
可用性和实现
FlaGs 可以从 https://github.com/GCA-VH-lab/FlaGs 下载，也可以在 http://www.webflags.se/ 在线运行。
补充信息
补充数据可在 Bioinformatics 在线获得。
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