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Frequently Asked Questions:

1. What if two or more MLST schemes are available for one species ?


2. Which sequence format is required for reference genome and query genome ?


3. How do I choose reference genome ? What if no reference genome is suitable for my isolate ?


4. How do I interpret the downloaded SNP file ? Which format should I follow to organize the uploaded SNP file ?


5. What if I want to submit dozens of isolates ?


6. Why is the downloaded file empty ?


7. How can I view .svg file ?

 

 


  What if two or more MLST schemes are available for one species ?
When multiple MLST schemes are available for one species, we recommend the one with lower resolution. The higher resolution tends to require more reference genomes, which are not necessary in most cases because the lower resolution is enough for distinguishing different lineages. In the current BacWGSTdb, Acinetobacter baumannii and Escherichia coli have two MLST schemes. We recommend the Pasteur scheme for A. baumannii and the UCC scheme for E. coli.
 

 

  Which sequence format is required for reference genome and query genome ?

The reference genome must be a single FASTA sequence. The query genome can be either single or multiple FASTA sequence.

 

  How do I choose reference genome ? What if no reference genome is suitable for my isolate ?

Two tools are provided for the selection of reference genome:

1) If the genome sequence of your isolate is available, either complete or draft one, use Determine-ST-by-genome. This tool will tell you which reference genome is suitable for your isolate and generate SNP data by comparing with the recommend reference genome;

 

2) When only the MLST Sequence Type (ST) is known for your isolate, use Choose-refgenome-by-ST. This tool will tell you which reference genome you should use for producing SNP data.

 

Your query isolate must belong to the same clonal complex to the reference genome. If no reference genome is suitable for your isolates, you can contact us and recommend adding new reference genomes to the database.

 
 

  How do I interpret the downloaded SNP file ? Which format should I follow to organize the uploaded SNP file ?

The SNP file follows the standard VCF format. The Variant Call Format (VCF) specifies the format of a plain text file used in bioinformatics for storing gene sequence variations. For more information about this format, please refer to Wikipedia. Both the downloaded and the uploaded SNP file follow the same format.


Note: plain text (*.txt) is required for the uploaded SNP file.

 

 

  What if I want to submit dozens of isolates ?
Don’t hesitate to contact us (Dr. Zhi Ruan). Probably what you need to do is to organize the provenance of your isolates into a table and sent it as well as the SNP data to us by email.
 

 

  Why is the downloaded file empty ?
Two reasons may lead to this problem. First, you give a wrong format of the input file. Second, your browser is likely to be incompatible with our database. At least IE, Firefox, Chrome and Safari work well on BacWGSTdb by our test.
 

 

  How can I view .svg file ?
Please open the phylogenetic tree file (.svg) with Internet browser, e.g., IE (9.0 or later), Firefox, Chrome and Safari. If you are running an old version of Internet browser, you may need to install a plugin of Adobe SVG Viewer.