基因顺序3.0：用于比较小型细菌基因组对中基因顺序的软件。

GeneOrder3.0: software for comparing the order of genes in pairs of small bacterial genomes.

作者信息

Celamkoti Srikanth, Kundeti Sashidhara, Purkayastha Anjan, Mazumder Raja, Buck Charles, Seto Donald

机构信息

Bioinformatics and Computational Biology, School of Computational Sciences, George Mason University, 10900 University Boulevard, MSN 5B3, Manassas, VA 20110, USA.

出版信息

BMC Bioinformatics. 2004 May 5;5:52. doi: 10.1186/1471-2105-5-52.

DOI:10.1186/1471-2105-5-52

PMID:15128433

原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC419981/

Abstract

BACKGROUND

An increasing number of whole viral and bacterial genomes are being sequenced and deposited in public databases. In parallel to the mounting interest in whole genomes, the number of whole genome analyses software tools is also increasing. GeneOrder was originally developed to provide an analysis of genes between two genomes, allowing visualization of gene order and synteny comparisons of any small genomes. It was originally developed for comparing virus, mitochondrion and chloroplast genomes. This is now extended to small bacterial genomes of sizes less than 2 Mb.

RESULTS

GeneOrder3.0 has been developed and validated successfully on several small bacterial genomes (ca. 580 kb to 1.83 Mb) archived in the NCBI GenBank database. It is an updated web-based "on-the-fly" computational tool allowing gene order and synteny comparisons of any two small bacterial genomes. Analyses of several bacterial genomes show that a large amount of gene and genome re-arrangement occurs, as seen with earlier DNA software tools. This can be displayed at the protein level using GeneOrder3.0. Whole genome alignments of genes are presented in both a table and a dot plot. This allows the detection of evolutionary more distant relationships since protein sequences are more conserved than DNA sequences.

CONCLUSIONS

GeneOrder3.0 allows researchers to perform comparative analysis of gene order and synteny in genomes of sizes up to 2 Mb "on-the-fly."

AVAILABILITY

http://binf.gmu.edu/genometools.html and http://pasteur.atcc.org:8050/GeneOrder3.0.

摘要

背景

越来越多的病毒和细菌全基因组被测序并存入公共数据库。随着对全基因组兴趣的增加，全基因组分析软件工具的数量也在增多。GeneOrder最初是为分析两个基因组之间的基因而开发的，可实现基因顺序可视化以及对任何小基因组进行共线性比较。它最初用于比较病毒、线粒体和叶绿体基因组。现在已扩展到大小小于2 Mb的小型细菌基因组。

结果

GeneOrder3.0已开发完成，并在NCBI GenBank数据库中存档的几个小型细菌基因组（约580 kb至1.83 Mb）上成功验证。它是一个基于网络的更新版“即时”计算工具，可对任何两个小型细菌基因组进行基因顺序和共线性比较。对几个细菌基因组的分析表明，如早期DNA软件工具所示，发生了大量的基因和基因组重排。这可以使用GeneOrder3.0在蛋白质水平上显示。基因的全基因组比对以表格和点阵图形式呈现。由于蛋白质序列比DNA序列更保守，这有助于检测进化上更远的关系。