trypdb analysis workflow
DESCRIPTION
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. - PowerPoint PPT PresentationTRANSCRIPT
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TrypDB Analysis Workflow
Common Analysis
T Cruzi Analysis
T Brucei Analysis
L BraziliensisAnalysis
L Infantum Analysis
L Major Analysis
Mercator
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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 NRDBShort Defline
Make Mercator Data Dir
Init apiSiteFilesRun Tuning
Manager
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Organism Analysis Workflow
Genome Analysis
Proteome Analysis
Make Data Dir
Make Gff FileRun Full Record
Dump
Init apiSiteFiles DownloadSite Organism Dir
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Genome Analysis
Extract Genome Seqs
Find Tandem Repeats
Load Tandem Repeats
Copy Genomic Seqs to Cluster
BLASTXNRDB
Filter Sequences
Load Low Complexity
Seqs
Splign
Make Data Dir
Dump and Block Mixed
Genome Seqs
Calculate Residues for NASequence
Make Mercator Gff File
tRNA Scan
DoTS Assemblies
ORFs
Misc DownloadSite
Files
Correct Reading Frame in
Mercator Gff file
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Proteome Analysis
Calcuate Protein Seq
Molecular Weight
Molecular Weight Min
Max
Isoelectric Point
Extract Protein Seqs
Filter Seqs
Load Low Complexity
Seqs
Copy Protein Seqs to Cluster
BLASTPNRDB
Psipred InterproScan
Run TMHMM
Load TMHMM
Run SignalP
Load SignalP
EpitopesFind Seq Identity to
NRDB
Load NRDB xrefs
BLASTPPDB
Make Data Dir
Make Annotated Protein
Download File
Update TaxonId for ExternalAASequence
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Make and Block Candidate
Assem Seqs
Make and Block DoTS
Assemblies
Map Candidate Assem Seqs to
Genome
Map DoTS Assemblies to
genome
Run Tuning Manager
Make DoTS Assemblies
Download File
DoTS Assemblies
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Make Derived CDS
Download File
Make EST Download
File
Make Transcript Download
File
Make Codon Usage
Download File
Misc DownloadSite Files
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Make ORFs
Load ORFs
Run Tuning Manager
Make ORF Download File
Make ORFNa Download File
ORFs
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BLAST
Make data dir
Start blast
Wait for cluster
Copy files From cluster
extract IDsFrom Blast
result
Load Subjectsubset
Load Result
Optional steps(runtime test)
filter by subject
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Psipred
fix protein IDsFor psipred
create psipredTask dir
copy Data Dirto cluster
start psipredOn cluster
wait for cluster
copy psipredFiles from
cluster
fix psipredFile names
make Alg Inv
load psipred
run pfilt on nrdb
Make data dir
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Splign
runSplign
Extract subjectSequenceAlt defline
insertSplign
Extract querySequenceAlt defline
Make Data Dir
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Epitopes
Make Data Dir
Make Blast Dir
Make protetins file
simple defline
Format NCBI blast file
Create Epitoptes map file
Load Epitopes map
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InterproScanMake 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
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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
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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 BlatAlignmentQuality
Table with Xml
Insert BLAT Alignment
Setbest BLAT Alignment
Start GFCluster Task
Wait for GF Cluster Task
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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
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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
Copy Genomic Separate Fasta Files
Map Assemblies to Genome
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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
Push Mixed Genomic Seq File to
Download File Dir
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Mercator
Run MercatorMavid
Create External Database and
Release for Synteny from Mercator
Insert Mercator Synteny Spans