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

 

◆mGenomeSubtractor

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 https://github.com/xavierdidelot/ClonalOrigin/wiki/Install
   
  ClonalOrigin: Inference of homologous recombination in bacteria using whole genome sequences 
  (Note:安装与使用方法来源于Xavierdidelot(https://github.com/xavierdidelot/ClonalOrigin/wiki/Usage, https://github.com/xavierdidelot/ClonalOrigin/wiki/Usage)
   
 
 
Phylogenetic tree build
  phyML, Rasxl, MEGA
 
Sequence alignment
  ClustalW, Musclue
 
Perl script for sequence analysis and genome comparison
  cds_faa.pl: extract CDS amino sequence from Genome annotation file (GenBank format);
  cds_fna.pl: extract CDS nucleotide sequence from Genome annotation file (GenBank format);
  fasta_header.pl: extract the sequence ID for a multiple sequence fasta file;
 
Usage for these perl ANI_bacth.pl:批量计算基因组平均核苷酸(ANI)
extractseuquence.pl:根据序列ID提取序列 ANI_bacth_patall.pl:批量计算基因组平均核苷酸(ANI),分割多cpu平行计算
blocksplit.pl:根据特定标示符分割文件 ani_vs.pl:处理 jspecies运算结果,以文本形式输出
cntPairwiseDiffs.pl Bacth_muscle.pl:多线程运行MUSCLE
cntSeqLen.pl catfasta2phyml.pl
Concat_Sequence.pl Cluster_blast.pl
gbf2tbl.pl:从gbk文件提取5列注释信息,用于基因组提交 core_blast.pl
test.pl hash_extract.pl: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
process.pl intersection.pl:多个文件列表,取交集
multi-thread.pl parallel_work.pl:多线程运行
multiple_tm.pl extract_protein_dir.pl:将目录文件夹的gbk,批量提取cds gene
FASTA_ID_mofied.pl extract_rRNA_dir.pl:从目录文件夹的gbk件,批量提取16S rRNA gene
extract_fas_from_gbk.pl extract_rRNA_sequence.pl:从目录文件夹的gbk件,批量提取rRNA gene (5S,23S,16S)
   
   

 

 
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