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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. Tc Specific Analysis. Tb Specific Analysis. Lm Specific Analysis. PlasmDB Analysis Workflow. Common Analysis. Pf Analysis. Py Analysis.

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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 TcSpecific Analysis Tb Specific Analysis Lm Specific Analysis

  2. PlasmDB Analysis Workflow Common Analysis Pf Analysis Py Analysis Pv Analysis Pc Analysis Pk Analysis Pv Mito Analysis Pg Analysis Pr Analysis Pf Specific Analysis Py Specific Analysis Pv Specific Analysis Pc Specific Analysis Pk Specific Analysis Pv Specific Analysis Pg Specific Analysis Pr Specific Analysis

  3. ToxoDB Analysis Workflow Common Analysis TgME49 Analysis TgVEG Analysis TgGT1 Analysis TgCkUg2 Analysis TgApicoplast Analysis Ncaninum Analysis TgME49 Specific Analysis TgVEG Specific Analysis TgGT1 Specific Analysis TgCkUg2 Specific Analysis TgApicoplast Specific Analysis Ncaninum Specific Analysis

  4. 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 Extract Isolate Seqs Make NRDB Short Defline Mirror Common Data Dir to Cluster

  5. Organism Analysis Workflow Make Data Dir Mirror Data Dir to Cluster Init apiSiteFilesDownloadSite Organism Dir Genome Analysis Proteome Analysis Optional steps Run Tuning Manager Make and Format Download Files

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

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

  8. BLAST Make data dir Make Task Input Dir Mirror Data Dir to Cluster Start blast filter by subject Wait for cluster extract IDs From Blast result Copy files From cluster Optional steps (runtime test) Load Subject subset Load Result

  9. TRNA Scan Make data dir Make Task Input Dir Mirror Data Dir to Cluster Start TRNA Scan Wait for cluster Copy files From cluster Load TRNA Scan

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

  12. 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

  13. Make and Block Candidate Assembly Seqs Make Candidate Assembly Seqs Make Candidate Assembly Seqs from Predicted Transcripts Make Data Dir Optional steps (runtime test) Extract Candidate Assembly Seqs Make Cluster Task Input Dir Mirror To Cluster Start Cluster Task Wait for Cluster Task Mirror From Cluster

  14. 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

  15. 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

  16. 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

  17. 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

  18. Pfalciparum Specific Analysis Run MUMMER for SNPs Su_SNPs Map SAGE Tags to Genome Seqs Run MUMMER for SNPs Broad_SNPs Load Anti-codon Run MUMMER for SNPs Winzeler_SNPs Map Oligos Run MUMMER for SNPs SangerPf_SNPs Run MUMMER for SNPs SangerPr_SNPs Run MUMMER for SNPs Combined_SNPs

  19. TgME49 Specific Analysis Run MUMMER for SNPs Stanford_SNPs Map SAGE Tags to Genome Seqs Map Oligos Run MUMMER for SNPs Sibley_SNPs Load Anti-codon ChIP-chip Run MUMMER for SNPs Nucmer_SNPs BlastnGenbank Isolates Blastn Sibley Isolates Map BAC Ends SeqstoGenome Map Cosmid Ends SeqstoGenome

  20. Map Oligos Extract OligoSeqs Extract Annotated Transcript Seqs Copy Transcripts Seqs to Cluster Copy OligoSeqs to Cluster BLAST Oligo Against Genomic Seqs BLAST Oligo Against Transcripts

  21. Blastn Isolate Seqs against Genome Seqs Extract IoslateSeqs Copy IoslateSeqs to Cluster BLAST Ioslate Against Genomic Seqs

  22. Map BAC Ends Seqs to Genome Seqs Make Data Dir Extract BAC Ends Seqs Make Repeat Mask Cluster Task Input Dir Mirror BAC ENDs Repeat Mask To Cluster Map BAC Ends Seqs to Genome Start RM Task on Cluster Wait for RM Cluster Task

  23. ChIP-chip Map ChIPseqs to Na Sequence Load mapping results

  24. Pyoelii Specific Analysis Map Oligos

  25. Run MUMMER for SNPs Copy Gff file from Download Extract Fasta file from Gff file Run Mummer Convert Mummer Result to Gff file Load Mummer Resoult

  26. Map SAGE Tags to Genome Seqs Extract SAGE Tag Seqs Map SAGE Tag seqs to Genome Seqs Load SAGE Tag Mapping Results Create SAGE Tag Normolization Files Load SAGE Tag Normalization Results

  27. 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

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