DroPPC Tutorial

DroPPC- A Drosophila Pipeline for Prediction of CRMs

29th Dec, 2010

DroPPC – User Input1. Go to home page: http://bioinf.gen.tcd.ie/DroPPC2. 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

DroPPC – Advanced User Input1. Click button to bring up advanced parameters

1. Modify settings, then click on green button to submit data

DroPPC – Sequence Retrieval1. DroPPC tries to match input to FlyBase transcript

1. Generates sequence file from default set of possible homologues

DroPPC – Sequence Retrieval1. For some Drosophila’s no homologue could be identified automatically2. Best possible candidates are listed in red, problem description as comment

1. Selection can be changed through checkboxes2. Click on the green button to finalize input file and select programs

DroPPC – Program Selection1. 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

DroPPC – Program Parameters1. For each program a variety of parameters can be modified

1. Select the type of combination required2. Click the green button to start the analysis

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

DroPPC – ResultsExplanation 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

DroPPC – Results1. 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