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SIPHT Workflow with P egasus

SIPHT Workflow with P egasus. Raphael B olze Karan Vahi. SIPHT Application . High throughput computational tool utilizing workflow management Conducts kingdom-wide predictions and annotations of intergenic sRNA -encoding genes.

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SIPHT Workflow with P egasus

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  1. SIPHT Workflow with Pegasus Raphael Bolze Karan Vahi

  2. SIPHT Application • High throughput computational tool utilizing workflow management • Conducts kingdom-wide predictions and annotations of intergenicsRNA-encoding genes. • Searches for putative sRNA-encoding genes in all 1640 bacterial replicons in the NCBI database. Ref: Livny J, Teonadi H, Livny M, Waldor MK (2008) High-Throughput, Kingdom-Wide Prediction and Annotation of Bacterial Non-Coding RNAs. PLoS ONE 3(9): e3197. doi:10.1371/journal.pone.0003197

  3. Overview of the SIPHT Application • Command line script : • Give input parameters • Hide all computational details • Launch single ROI annotation • Launch annotation for all ROI • Web user portal : • Use the same script • Receive email with result when computation is done DAX generator Pegasus Planner Computational resources: Condor pool, TeraGrid, OSG, Cloud …

  4. Pre-compute works NCBI_Fetch i: inputs (~410 MB) o: outputs (~34MB) IRGExtract3 TFBS matrices RNAMotif i:22 o:2 FindTerm i:3 o:9 Transterm i:4 o:2 Blast i:1643 o:3 Patser Dynamic tasks i:5 o:1 SRNA i:11 o:14 FFN_parser i:5 o:3 Blast_candidate i:2 o:3 Blast_paralogues i:5 o:3 Blast_QRNA i:1649 o:8 Patser_Concate i: 20 o:1 Blast_synteny i:6 o:3 SRNA_annotate i:10 o:9 Pegasus DAX

  5. Web portal interface http://newbio.cs.wisc.edu/sRNA/

  6. SIPHT workflow with Pegasus GUI

  7. Output of the SIPHT applicationsRNA annotated

  8. SIPHT Workflow Gantt Chart

  9. Annotate all ROI (1640)(recursive DAX)

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