1. DroPPC Tutorial DroPPC- A Drosophila Pipeline for Prediction of CRMs 29 th Dec, 2010

2. DroPPC – User Input 1.Go to home page: http://bioinf.gen.tcd.ie/DroPPChttp://bioinf.gen.tcd.ie/DroPPC 2.Insert a gene name (e.g. eve) or FlyBase ID (gene or transcript) into field 3.Click on green button to submit data or click button to bring up more options

3. DroPPC – Advanced User Input 1.Click button to bring up advanced parameters 1.Modify settings, then click on green button to submit data

4. DroPPC – Sequence Retrieval 1.DroPPC tries to match input to FlyBase transcript 1.Generates sequence file from default set of possible homologues

5. DroPPC – Sequence Retrieval 1.For some Drosophila’s no homologue could be identified automatically 2.Best possible candidates are listed in red, problem description as comment 1.Selection can be changed through checkboxes 2.Click on the green button to finalize input file and select programs

6. DroPPC – Program Selection 1.Tick boxes of all the programs you would like to run 1.Click on the green button to start analysis or other button for more parameters

7. DroPPC – Program Parameters 1.For each program a variety of parameters can be modified 1.Select the type of combination required 2.Click the green button to start the analysis

8. DroPPC – Results 1.Webpage will update until all results are available 2.Input sequence file can be downloaded 3.Results from individual programs are available but hidden 4.Combination of results is listed in full 5.Sites from RedFly are listed if they overlap with input regions

9. DroPPC – Results Explanation of tracks: 1.RedFly sites (if available) 2.WeederH predictions 3.PhyloGibbs predictions 4.FootPrinter predictions 5.Combined sites from all programs 6.Combined sites merged down to nucleotide level 7.Overlap with RedFly sites

10. DroPPC – Results 1.Metrics for comparison or results with RedFly sites (if available) 2.Listing of combined sites including sequence and program support 3.Link to download combined results