 | Convert data |
Transformation of TransTermHP,
CRISPRfinder,
MOSAIC,
PatScan,
DARN! (GFF),
GenBank output data
in GFF and GAME XML format data that can be read by Apollo.
Launch conversion
Note 1: The indications of translation table (/transl_table) of the GenBank files are removed in the GAME XML file because Apollo does not take into account alternative translation tables. When they are mentioned, CDS is not displayed.
Note 2: The related genomic sequence positions are necessary for Apollo to correctly manage the positions of the data when an another layer of data is added. When the new data does not cover all the related genomic sequence, Apollo cuts the yet loaded genomic sequence from the beginning of the first element to the end of the last element of the data added. To avoid this problem, we declare two artefact elements at the beginning and the end of the related sequence.
How to get input data
Getting TransTermHP data
Go to the
TransTermHP page.
Click an organism.
Copy and paste the whole displaying result.
Getting CRISPRfinder data
Go to the
CRISPRfinder page.
Submit your data and launch CRISPRfinder.
In the left menu, click "Save files" link.
Copy and paste the whole displaying text.
Getting MOSAIC data
Go to the
MOSAIC page.
Select a species and click the "Submit" button.
Click a "Select this alignment" button.
In the View column (on the right), click the "Loops" link.
In the opened window, select "coordinates" radio button and click the "for all listed loops" button.
Copy and paste the whole displaying text.
Getting PatScan data
Go to the
PatScan page.
Fill the fields and click the "Submit" button.
In your mailbox, open the PatScan email.
Copy and paste the whole body of the email.
Getting GFF DARN! data
Go to the
DARN! page.
Enter a descriptor and a main sequence.
In the options, select the "Use GFF format to output solutions" checkbox.
Click the "GO!" button.
Copy and paste the whole displaying result.
Getting GenBank data
Go to the
NCBI ftp.
Go to the directory of your choice.
Click a GenBank file (.gbk).
Copy and paste the whole displaying result.
How to visualize output data
Visualizing GFF data in Apollo
Copy and paste the resulting text in a new file, whose name has the extension .gff.
Launch Apollo.
In the list 'Choose data source', choose 'Ensembl GFF file format' and load the new GFF file.
Click the "OK" button.
Visualizing GAME XML data in Apollo
Copy and paste the resulting text in a new file, whose name has the extension .xml.
Launch Apollo.
In the list 'Choose data source', choose 'GAME XML format' and load a first GAME XML file (containing at least the genomic sequence).
Click the "OK" button.
In the File menu, click 'Layer more results or annotations...'.
In the list 'Choose data source', choose 'GAME XML format' and load the new GAME XML file (without the genomic sequence).
Click the "OK" button.
Last update: February 17, 2010.