Bacterial Genome Data mining & Bioinformatic Analysis
Curriculum vitae for Dr. Xiangyang Li
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Genome and genome annotation

Prophase work for microbe genome analysis

General motive for genome sequencs determinations: 1) Bacterium you isolated inclues specific feather you focused; 2) Bacterium classification due to dysfunction of traditional methods (like 16S rRNA); 3) Genome evolution (or dynamic) analaysis (like, movement of pathogenicity assciated with genes and bacterial speciation).

Second high-throughout seqeuncing: 1) solic-454, the length per read is around 400bp; 2) illuminas, the length per read is around 100bp. Generally, this process is finished by company. and you can obtain the assembly sequence information from commercial company (such as contigs or scof).

Micorbial genome annotation procedure

Genome annotation:

There are many channels used for genome annotation: manual annotation and auto-annotation, we recommend auto-annotation based method: like PGAP (prokaryotic genome annotation pipline) and RAST high-quelity annotation for reseachers with little or no knowledge on Computer or Bioinformatics.

Protein function cluter:

Predicted proteimic of genome was group according to metobolism function. like COG and KO clutering analysis.

Other specific analysis:

Insertion sequence (IS), repeat sequence, genomic island (GI), prophage, secondary matobolism products...

 

 
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