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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. Run Tuning Manager. 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 Run Tuning Manager Make Data Dir Init User/Group/Project Init apiSiteFiles 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 Init apiSiteFilesDownloadSiteOrganism Dir Genome Analysis Proteome Analysis Make Gff File Run Full Record Dump

  4. Genome Analysis Calculate Residues for NASequence Make Data Dir Misc DownloadSite Files Make Mercator Gff File Dump and Block Mixed Genome Seqs Extract Genome Seqs Splign Correct Reading Frame in Mercator Gff file DoTS Assemblies ORFs Copy Genomic Seqs to Cluster Find Tandem Repeats Filter Sequences tRNA Scan BLASTX NRDB Load Low Complexity Seqs Load Tandem Repeats

  5. Proteome Analysis Calcuate Protein Seq Make Data Dir Update TaxonId for ExternalAASequence Make Annotated Protein Download File Molecular Weight Min Max Molecular Weight Isoelectric Point 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. DoTS Assemblies Make and Block Candidate AssemSeqs Map Candidate Assem Seqs to Genome Make and Block DoTS Assemblies Map DoTS Assemblies to genome Run Tuning Manager Make DoTSAssemblies Download File

  7. Misc DownloadSite Files Make Derived CDS Download File Make EST Download File Make Transcript Download File Make Codon Usage Download File

  8. ORFs Make ORFs Load ORFs Run Tuning Manager Make ORF Download File Make ORFNa Download File

  9. 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 Load Result

  10. 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

  11. Splign Make Data Dir Extract query Sequence Alt defline Extract subject Sequence Alt defline runSplign insertSplign

  12. Epitopes Make Data Dir Make Blast Dir Make protetins file simple defline Format NCBI blast file Create Epitoptes map file Load Epitopes map

  13. 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 Make Interpro Download File

  14. 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

  15. Map Candidate Assembly Seqs to Genome Make Data Dir Insert BlatAlignmentQuality Table with Xml Extract Genomic Seqs into Separate Fasta Files Make Gf Client Cluster Task Input Dir Mirror Gf Client to Cluster Start GFCluster Task Wait for GF Cluster Task Mirror Gf Client From Cluster Insert BLAT Alignment Setbest BLAT Alignment

  16. 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

  17. Map Assemblies to Genome Make Data Dir Make Assembly Gf Client Cluster Task Input Dir Copy Genomic Separate Fasta Files 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

  18. 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 Push Mixed Genomic Seq File to Download File Dir Start Cluster Task Wait for Cluster Task Mirror Virtual Sequence Repeat Mask From Cluster Move Blocked Seq File to Mercator Data Dir

  19. Mercator Run MercatorMavid Create External Database and Release for Synteny from Mercator Insert Mercator Synteny Spans

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