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TrypDB Analysis Workflow

TrypDB Analysis Workflow. Common Analysis. T Cruzi Analysis. T Brucei Analysis. L Braziliensis Analysis. L Infantum Analysis. L Major Analysis. Mercator. Common Analysis. Init Workflow Home Dir on Cluster. Init apiSiteFiles WebServices Dirs. Make Data Dir. Init User/Group/Project.

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TrypDB Analysis Workflow

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  1. TrypDB Analysis Workflow Common Analysis T Cruzi Analysis T Brucei Analysis L Braziliensis Analysis L Infantum Analysis L Major Analysis Mercator

  2. Common Analysis Init Workflow Home Dir on Cluster Init apiSiteFilesWebServicesDirs Make Data Dir Init User/Group/Project Insert BlatAlignmentQuality Table with Xml Copy PDB from Downloads Copy NRDB from Downloads Make Mercator Data Dir Make NRDB Short Defline Mirror Common Data Dir to Cluster

  3. Organism Analysis Workflow Make Data Dir Mirror Data Dir to Cluster Init apiSiteFilesDownloadSite Organism Dir Genome Analysis Proteome Analysis Run Tuning Manager Run Full Record Dump Make Gff File Make and Format Download Files

  4. Genome Analysis Make Data Dir Dump and Block Mixed Genome Seqs Extract Genome Seqs Make and Block Candidate Assem Seqs Copy Genomic Seqs to Cluster Find Tandem Repeats Make ORFs Filter Sequences tRNA Scan Map Candidate Assem Seqs to Genome Load ORFs BLASTX NRDB Load Low Complexity Seqs Load Tandem Repeats Make and Block DoTS Assemblies Map DoTS Assemblies to genome

  5. Proteome Analysis Calcuate Protein Seq Make Data Dir Update TaxonId for PDB ExternalAASequence Calculate AASeq Attributes Extract Protein Seqs Find Seq Identity to NRDB Filter Seqs Run TMHMM Run SignalP Epitopes Load NRDB xrefs Load Low Complexity Seqs Copy Protein Seqs to Cluster Load TMHMM Load SignalP BLASTP NRDB Psipred InterproScan BLASTP PDB

  6. BLAST Make data dir Start blast Wait for cluster Copy files From cluster filter by subject extract IDs From Blast result Optional steps (runtime test) Load Subject subset Update TaxonId for Nrdb ExternalAASequence Load Result

  7. Psipred Make data dir fix protein IDs For psipred run pfilt on nrdb create psipred Task dir copy Data Dir to cluster start psipred On cluster wait for cluster copy psipred Files from cluster make Alg Inv fix psipred File names load psipred

  8. Epitopes Make Data Dir Make Blast Dir Format NCBI blast file Create Epitoptes map file Load Epitopes map

  9. InterproScan Make Data Dir Make InterproScan Cluster Task Input Dir Mirror InterproScan to Cluster Start Cluster Task Wait for Cluster Task Mirror InterproScan From Cluster Insert IprScan Results

  10. Make and Block Candidate Assembly Seqs Make Candidate Assembly Seqs Make Data Dir Extract Candidate Assembly Seqs Make Cluster Task Input Dir Mirror To Cluster Start Cluster Task Wait for Cluster Task Mirror From Cluster

  11. Map Candidate Assembly Seqs to Genome Make Data Dir Extract Genomic Seqs into Separate Fasta Files Make Gf Client Cluster Task Input Dir Mirror Gf Client to Cluster Run Nib On Cluster Start GFCluster Task Wait for GF Cluster Task Mirror Gf Client From Cluster Insert BLAT Alignment Setbest BLAT Alignment

  12. Make and Block Assemblies Make Data Dir Make Repeat Mask Cluster Task Input Dir Cluster Transcripts by Genome Alignment Put Unaligned Transcripts into One Cluster Assemble Transcripts Extract Assemblies Mirror Assembly Repeat Mask To Cluster Start RM Task on Cluster Wait for RM Cluster Task

  13. Map Assemblies to Genome Make Data Dir Make Assembly Gf Client Cluster Task Input Dir Mirror Assembly Gf Client to Cluster Start GF Task on Cluster Wait for GF Cluster Task Mirror Gf Client From Cluster Insert BLAT Alignment Setbest BLAT Alignment Update Assembly Source Id

  14. Dump and Block Mixed Genome Seqs Make Data Dir Dump Mixed Genomic Sequences Make Repeat Mask Cluster Task Input Dir Mirror Repeat Mask To Cluster Start Cluster Task Wait for Cluster Task Mirror Virtual Sequence Repeat Mask From Cluster Move Blocked Seq File to Mercator Data Dir

  15. Mercator Make Mercator Gff File Correct Reading Frame in Mercator Gff file Run MercatorMavid Create External Database and Release for Synteny from Mercator Insert Mercator Synteny Spans

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