GCModeller [version 1.0.0.0]

Module AssemblyName: file:///G:/GCModeller/manual/bin/mpl.exe
Root namespace: xMPAlignment.CLI

All of the command that available in this program has been list below:

Function API Info
/Build.Db.CDD Install NCBI CDD database into the GCModeller repository database for the MPAlignment analysis.
/Build.Db.Family Build protein family database from KEGG database dump data and using for the protein family annotation by MPAlignment.
/Build.Db.Family.Manual-Build
/Build.Db.Ortholog Build protein functional orthology database from KEGG orthology or NCBI COG database.
/Build.Db.PPI Build protein interaction seeds database from string-db.
/Build.PPI.Signature
/KEGG.Family
/Motif.Density
/Pfam.Align Align your proteins with selected protein domain structure database by using blast+ program.
/Pfam.Sub
/Pfam-String.Dump Dump the pfam-String domain Structure composition information from the blastp alignment result.
/Select.Pfam-String
–align MPAlignment on your own dataset.
–align.Family Protein family annotation by using MPAlignment algorithm.
–align.Family_test
–align.Function Protein function annotation by using MPAlignment algorithm.
–align.PPI Protein-Protein interaction network annotation by using MPAlignment algorithm.
–align.PPI_test
–align.String MPAlignment test, pfam-string value must be in format as ::
–blast.allhits
–View.Alignment

Commands


Help for command ‘/Build.Db.CDD’:

Prototype: xMPAlignment.CLI::Int32 InstallCDD(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Install NCBI CDD database into the GCModeller repository database for the MPAlignment analysis.
Usage: G:\GCModeller\manual\bin\mpl.exe /Build.Db.CDD /source <source.DIR>
Example: mpl /Build.Db.CDD
Help for command ‘/Build.Db.Family’:

Prototype: xMPAlignment.CLI::Int32 BuildFamily(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Build protein family database from KEGG database dump data and using for the protein family annotation by MPAlignment.
Usage: G:\GCModeller\manual\bin\mpl.exe /Build.Db.Family /source <source.KEGG.fasta> /pfam <pfam-string.csv>
Example: mpl /Build.Db.Family
Help for command ‘/Build.Db.Family.Manual-Build’:

Prototype: xMPAlignment.CLI::Int32 ManualBuild(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\mpl.exe /Build.Db.Family.Manual-Build /pfam-string <pfam-string.csv> /name <familyName>
Example: mpl /Build.Db.Family.Manual-Build
Help for command ‘/Build.Db.Ortholog’:

Prototype: xMPAlignment.CLI::Int32 BuildOrthologDb(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Build protein functional orthology database from KEGG orthology or NCBI COG database.
Usage: G:\GCModeller\manual\bin\mpl.exe /Build.Db.Ortholog [/COG <cogDIR> /KO]
Example: mpl /Build.Db.Ortholog
Help for command ‘/Build.Db.PPI’:

Prototype: xMPAlignment.CLI::Int32 BuildPPIDb(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Build protein interaction seeds database from string-db.
Usage: G:\GCModeller\manual\bin\mpl.exe
Example: mpl /Build.Db.PPI
Help for command ‘/Build.PPI.Signature’:

Prototype: xMPAlignment.CLI::Int32 BuildSignature(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\mpl.exe /Build.PPI.Signature /in <clustalW.fasta> [/level <5> /out <out.xml>]
Example: mpl /Build.PPI.Signature

Parameters information:

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   [/level]
Description: It is not recommended to modify this value. The greater of this value, the more strict of the interaction scoring. level 5 is enough.

Example: /level ""

Accepted Types

/level
Help for command ‘/KEGG.Family’:

Prototype: xMPAlignment.CLI::Int32 KEGGFamilys(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\mpl.exe /KEGG.Family /in <inDIR> /pfam <pfam-string.csv> [/out <out.csv>]
Example: mpl /KEGG.Family
Help for command ‘/Motif.Density’:

Prototype: xMPAlignment.CLI::Int32 MotifDensity(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\mpl.exe /Motif.Density /in <pfam-string.csv> [/out <out.csv>]
Example: mpl /Motif.Density
Help for command ‘/Pfam.Align’:

Prototype: xMPAlignment.CLI::Int32 AlignPfam(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Align your proteins with selected protein domain structure database by using blast+ program.
Usage: G:\GCModeller\manual\bin\mpl.exe /Pfam.Align /query <query.fasta> [/db <name/path> /out <blastOut.txt>]
Example: mpl /Pfam.Align
Help for command ‘/Pfam.Sub’:

Prototype: xMPAlignment.CLI::Int32 SubPfam(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\mpl.exe /Pfam.Sub /index <bbh_index.csv> /pfam <pfam-string> [/out <sub-out.csv>]
Example: mpl /Pfam.Sub
Help for command ‘/Pfam-String.Dump’:

Prototype: xMPAlignment.CLI::Int32 DumpPfamString(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Dump the pfam-String domain Structure composition information from the blastp alignment result.
Usage: G:\GCModeller\manual\bin\mpl.exe /Pfam-String.Dump /In <blastp_out.txt> [/out <pfam-String.csv> /evalue <0.001> /identities <0.2> /coverage <0.85>]
Example: mpl /Pfam-String.Dump

Parameters information:

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 /In
Description: The blastp output For the protein alignment, which the aligned database can be selected from Pfam-A Or NCBI CDD. And blast+ program Is recommended For used For the domain alignment.

Example: /In ""

[/out]
Description: The output Excel .csv data file path For the dumped pfam-String data Of your annotated protein. If this parameter Is empty, Then the file will saved On the same location With your blastp input file.

Example: /out ""

Accepted Types

/In
/out
Help for command ‘/Select.Pfam-String’:

Prototype: xMPAlignment.CLI::Int32 SelectPfams(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\mpl.exe /Select.Pfam-String /in <pfam-string.csv> /hits <bbh/sbh.csv> [/hit_name /out <out.csv>]
Example: mpl /Select.Pfam-String
Help for command ‘–align’:

Prototype: xMPAlignment.CLI::Int32 MPAlignment(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  MPAlignment on your own dataset.
Usage: G:\GCModeller\manual\bin\mpl.exe --align /query <pfam-string.csv> /subject <pfam-string.csv> [/hits <query_vs_sbj.blastp.csv> /flip-bbh /out <alignment_out.csv> /mp <cutoff:=0.65> /swap /parts]
Example: mpl --align

Parameters information:

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       [/swap]
Description: Swap the location of query and subject in the output result set.

Example: /swap ""

[/parts]
Description: Does the domain motif equals function determine the domain positioning equals just if one side in the high scoring then thoese two domain its position is equals?
Default is not, default checks right side and left side.

Example: /parts ""

[/flip-bbh]
Description: Swap the direction of the query_name/hit_name in the hits?

Example: /flip-bbh ""

Accepted Types

/swap
/parts
/flip-bbh
Help for command ‘–align.Family’:

Prototype: xMPAlignment.CLI::Int32 FamilyClassified(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Protein family annotation by using MPAlignment algorithm.
Usage: G:\GCModeller\manual\bin\mpl.exe --align.Family /query <pfam-string.csv> [/out <out.csv> /threshold 0.5 /mp 0.6 /Name <null>]
Example: mpl --align.Family

Parameters information:

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   [/Name]
Description: The database name of the aligned subject, if this value is empty or not exists in the source, then the entired Family database will be used.

Example: /Name ""

Accepted Types

/Name
Help for command ‘–align.Family_test’:

Prototype: xMPAlignment.CLI::Int32 FamilyAlignmentTest(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\mpl.exe --align.Family_test /query <pfam-string> /name <dbName/Path> [/threshold <0.65> /mpCut <0.65> /accept <10>]
Example: mpl --align.Family_test
Help for command ‘–align.Function’:

Prototype: xMPAlignment.CLI::Int32 AlignFunction(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Protein function annotation by using MPAlignment algorithm.
Usage: G:\GCModeller\manual\bin\mpl.exe
Example: mpl --align.Function
Help for command ‘–align.PPI’:

Prototype: xMPAlignment.CLI::Int32 MplPPI(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  Protein-Protein interaction network annotation by using MPAlignment algorithm.
Usage: G:\GCModeller\manual\bin\mpl.exe
Example: mpl --align.PPI
Help for command ‘–align.PPI_test’:

Prototype: xMPAlignment.CLI::Int32 StructureAlign(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\mpl.exe --align.PPI_test /query <contacts.fasta> /db <ppi_signature.Xml> [/mp <cutoff:=0.9> /out <outDIR>]
Example: mpl --align.PPI_test
Help for command ‘–align.String’:

Prototype: xMPAlignment.CLI::Int32 MPAlignment2(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  MPAlignment test, pfam-string value must be in format as  <locusId>:<length>:<pfam-string>
Usage: G:\GCModeller\manual\bin\mpl.exe --align.String /query <pfam-string> /subject <pfam-string> [/mp <cutoff:=0.65> /out <outDIR> /parts]
Example: mpl --align.String
Help for command ‘–blast.allhits’:

Prototype: xMPAlignment.CLI::Int32 ExportAppSBH(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\mpl.exe --blast.allhits /blast <blastp.txt> [/out <sbh.csv> /coverage <0.5> /identities 0.15]
Example: mpl --blast.allhits
Help for command ‘–View.Alignment’:

Prototype: xMPAlignment.CLI::Int32 ViewAlignment(Microsoft.VisualBasic.CommandLine.CommandLine)

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Information:  
Usage: G:\GCModeller\manual\bin\mpl.exe --View.Alignment /blast <blastp.txt> /name <queryName> [/out <out.png>]
Example: mpl --View.Alignment