Bacterial Genome Data mining & Bioinformatic Analysis
Curriculum vitae for Dr. Xiangyang Li
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Chinese Version [中文版]
Biolinux (Linux system, which has preinstalled a lots of softewares for bioinformatics), the detailed install information could refer to the UBUNTU
Genome comaprison software:
  Mauve (multiple genome alignments);
  MUMmer (Ultra-fast alignment of large-scale DNA and protein sequences), which was used to 1) comapred a pair of genoms with a rapid rate; 2) interference the synteny of genomes; 3) SNP analysis; 4) reorder the sequence of the contigs for draft genome using referance genome.
  Local Blast: very useful tools for genome comparison, like specif genes and core genome identifed for multiple genomes
  ACT (Artemis Comparison Tool, comparison of a pair of genomes)
Inquire the Number of Genome Sequences
◆Draft (WGS) Genome ◆Complete Genome
Genome Data Retrive
  ◆Pleasee click here
Genome Blast
  ◆TBLASTN search translated nucleotide databases using a protein query
Web Based Genome Comparison



If you used this server in your study, plase cite this reference: Shao Y, He X, Harrison EM, Tai C, Ou HY, Rajakumar K, Deng Z. mGenomeSubtractor: a web-based tool for parallel in silico subtractive hybridization analysis of multiple bacterial genomes.Nucleic Acids Res. 2010 Jul;38(Web Server issue):W194-200

Serveral powerfule softwares to infer genomic flux pattren
  ClonalFrame: Inference of bacterial microevolution using multilocus sequence date
  ClonalFrameML: Efficient inference of recombination in whole bacterial genomes
  GenoPlast: Inference of homologous recombination in bacteria using whole genome sequences
                 download from
  ClonalOrigin: Inference of homologous recombination in bacteria using whole genome sequences 
Phylogenetic tree build
  phyML, Rasxl, MEGA
Sequence alignment
  ClustalW, Musclue
Perl script for sequence analysis and genome comparison extract CDS amino sequence from Genome annotation file (GenBank format); extract CDS nucleotide sequence from Genome annotation file (GenBank format); extract the sequence ID for a multiple sequence fasta file;
Usage for these perl批量计算基因组平均核苷酸(ANI)根据序列ID提取序列批量计算基因组平均核苷酸(ANI),分割多cpu平行计算根据特定标示符分割文件处理 jspecies运算结果,以文本形式输出多线程运行MUSCLE从gbk文件提取5列注释信息,用于基因组提交以blast结果为输入文件,转换,提输出N个基因组的共同核心基因组序列文件多个文件列表,取交集多线程运行将目录文件夹的gbk,批量提取cds gene从目录文件夹的gbk件,批量提取16S rRNA gene从目录文件夹的gbk件,批量提取rRNA gene (5S,23S,16S)


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