SourceForge IceCafe project Top
ICE Café
1. About Ice café
Ice café is a software for viewing sequence chromatgram, and measuring peak intensity of each peaks.
Ice café is firstly developed for the purpose of detecting RNA Editing using ICE method. However, ICE café
also can be used when one uses conventional RNA Editing detection method in which genomic chromatgram is compared to
that of mRNA.
ICE metothod and ICE Cafe are developed at Suzuki Lab at Dept Chem&Biotech Tokyo University.
file directory
2. file setting
Ice café read ace file, which is the output file from phred/phrap/consed (http://www.phrap.org/).
There should be following three folder to be prepared before using Ice café, which can be prepared
by direct output of phred/phrap/consed .
The folders are:
phd_dir : phred called datafiles are placed here
edit_dir : Ace file is should be placed here
chromat_dir : chromatgram files are placed here
Pls check out sample data files for file configrations.
3 To launch Ice café, click Icecafé.bat file, after extract archive Ice café file.
Java runtime environment should be installed before executing Ice café.
(http://www.java.com/)
4 Select Ice file
After selecting acefile, alginments list are displayed in combo box.
Select Alginment and click “Ice café View”
5 Find out genomic position
After clicking button built in browser with consensus/reference sequence at the top
will show up with Blat search URL at UCSC.
Copy and paste sequence, and submit (inside the browser) to execute blat search.
Display details and push “Parse Data” button
Alternatively, you can input
chr, strand, position
manually.
6. Push “goto Ice café ” botton
note:
- Make sure non ICE treated sequence cromatgram are displayed at the top, if not please adjust position by
choosing sequence cromatgram index at cobmbo box and clicking “UP” or “Down” button.
- Upper window display cromatgram and Lower window display A and G peak intensity and base call quality for each base.
- Ice café detect Editing by applying filter 1 to 4, Users can chose filter and see the result by
clicking “Apply filter” button. Filter value can be modified by “Setting property”
- Exact A/G ratio value can be viewed by “Data Grid”
-cromat gram graph can be 're adjusted' by double clicking Cromat Graph at desired position.
7. Filterling and finding RNA Editing
Ice café implement an automatic RNA Editing detection functionality by conditional flow
using peak intensity and base call quality.
Each thresholding values can be set by Property Editer.
And Ice café can have 4 filter having different threshold values.
8. Manual correction/checking
Even Ice café having RNA Editng detection functions, it is often difficult
to detect a genuine RNA Editng when cromatgram quality is low or
consecutive G peak exist near A site.
Right click to display the status which you want to change after manual eye checking,
and select the status.
9 click data grid to display A to G ratio.
