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 User/Group/Project Copy PDB from Downloads Make Data Dir Mirror Common Data Dir to Cluster Copy NRDB from Downloads Make NRDB Short Defline Make Mercator Data Dir Init apiSiteFiles WebServices Dirs Insert BlatAlignmentQuality Table with Xml

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

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

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

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

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

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

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

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

13. 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 Map Assemblies to Genome

14. 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 Make Data Dir Dump and Block Mixed Genome Seqs Move Blocked Seq File to Mercator Data Dir

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