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NAME

InfoAminoAcids.pl - List properties of amino acids

SYNOPSIS

InfoAminoAcids.pl AminoAcidIDs...

InfoAminoAcids.pl [-h, --help] [--outdelim comma | tab | semicolon] [--output STDOUT | File] [--outputstyle AminoAcidBlock | AminoAcidRows] [-o, --overwrite] [--precision number] [--propertiesmode Categories | Names | All] [-p, --properties CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]] [--propertieslinting ByGroup | Alphabetical] [-q, --quote yes | no] [-r, --root rootname] [-w, --workingdir dirname] AminoAcidIDs...

DESCRIPTION

List amino acid properties. Amino acids identification supports these three types of IDs: one letter code, three letter code or name. Amino acid properties data, in addition to basic information about amino acids - one and three letter codes, name, DNA and RNA codons, molecular weight - include variety of other properties: polarity, acidity, hydrophobicity, and so on.

PARAMETERS

AminoAcidIDs ThreeLetterCode [OneLetterCode AminoAcidName...]

AminoAcidIDs is a space delimited list of values to identify amino acids.

Input value format is: ThreeLetterCode [OneLetterCode AminoAcidName...]. Default: Ala. Examples:

Ala
Glu A
Alanine Glu Y "Aspartic acid"

OPTIONS

-h, --help

Print this help message.

--outdelim comma | tab | semicolon

Output text file delimiter. Possible values: comma, tab, or semicolon Default value: comma.

--output STDOUT | File

List information at STDOUT or write it to a file. Possible values: STDOUT or File. Default: STDOUT. -r, --root option is used to generate output file name.

--outputstyle AminoAcidBlock | AminoAcidRows

Specify how to list amino acid information: add a new line for each property and present it as a block for each amino acid; or include all properties in one line and show it as a single line.

Possible values: AminoAcidBlock | AminoAcidRows. Default: AminoAcidBlock

An example for AminoAcidBlock output style:

ThreeLetterCode: Ala
OneLetterCode: A
AminoAcid: Alanine
MolecularWeight: 89.0941
... ...
... ...
... ...
ThreeLetterCode: Glu
OneLetterCode: E
AminoAcid: Glutamic acid
MolecularWeight: 147.1308
... ...
... ...
... ...

An example for AminoAcidRows output style:

ThreeLetterCode,OneLetterCode,AminoAcid,MolecularWeight
Ala,A,Alanine,89.0941..
Glu,E,Glutamic acid,147.1308..
-o, --overwrite

Overwrite existing files.

--precision number

Precision for listing numerical values. Default: up to 4 decimal places. Valid values: positive integers.

--propertiesmode Categories | Names | All

Specify how property names are specified: use category names; explicit list of property names; or use all available properties. Possible values: Categories, Names, or All. Default: Categories.

This option is used in conjunction with -p, --properties option to specify properties of interest.

-p, --properties CategoryName,[CategoryName,...] | PropertyName,[PropertyName,...]

This option is --propertiesmode specific. In general, it's a list of comma separated category or property names.

Specify which amino acid properties information to list for the amino acid IDs specified using command: line parameters: list basic and/or hydrophobicity information; list all available information; or specify a comma separated list of amino acid property names.

Possible values: Basic | BasicPlus | BasicAndHydrophobicity | BasicAndHydrophobicityPlus | PropertyName,[PropertyName,...]. Default: Basic.

Basic includes: ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4

BasicPlus includes: ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, AcidicBasic, PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic, IsoelectricPoint, pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight, ExactMass, ChemicalFormulaMinusH2O, MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056), LinearStructure, LinearStructureAtpH7.4

BasicAndHydrophobicity includes: ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4, HydrophobicityEisenbergAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin, HydrophobicityKyteAndDoolittle, HydrophobicityRoseAndOthers, HydrophobicityWolfendenAndOthers

BasicAndHydrophobicityPlus includes: (ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, ChemicalFormula, MolecularWeight, LinearStructure, LinearStructureAtpH7.4, HydrophobicityAbrahamAndLeo, HydrophobicityBlack, HydrophobicityBullAndBreese, HydrophobicityChothia, HydrophobicityEisenbergAndOthers, HydrophobicityFauchereAndOthers, HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan, HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers, HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin, HydrophobicityKyteAndDoolittle, HydrophobicityManavalanAndOthers, HydrophobicityMiyazawaAndOthers, HydrophobicityOMHSweetAndOthers, HydrophobicityRaoAndArgos, HydrophobicityRfMobility, HydrophobicityRoseAndOthers, HydrophobicityRoseman, HydrophobicityWellingAndOthers, HydrophobicityWolfendenAndOthers

Here is a complete list of available properties: ThreeLetterCode, OneLetterCode, AminoAcid, DNACodons, RNACodons, AcidicBasic, PolarNonpolar, Charged, Aromatic, HydrophobicHydophilic, IsoelectricPoint, pKCOOH, pKNH3+, ChemicalFormula, MolecularWeight, ExactMass, ChemicalFormulaMinusH2O, MolecularWeightMinusH2O(18.01524), ExactMassMinusH2O(18.01056), vanderWaalsVolume, %AccessibleResidues, %BuriedResidues, AlphaHelixChouAndFasman, AlphaHelixDeleageAndRoux, AlphaHelixLevitt, AminoAcidsComposition, AminoAcidsCompositionInSwissProt, AntiparallelBetaStrand, AverageAreaBuried, AverageFlexibility, BetaSheetChouAndFasman, BetaSheetDeleageAndRoux, BetaSheetLevitt, BetaTurnChouAndFasman, BetaTurnDeleageAndRoux, BetaTurnLevitt, Bulkiness, CoilDeleageAndRoux, HPLCHFBARetention, HPLCRetentionAtpH2.1, HPLCRetentionAtpH7.4, HPLCTFARetention, HydrophobicityAbrahamAndLeo, HydrophobicityBlack, HydrophobicityBullAndBreese, HydrophobicityChothia, HydrophobicityEisenbergAndOthers, HydrophobicityFauchereAndOthers, HydrophobicityGuy, HydrophobicityHPLCAtpH3.4Cowan, HydrophobicityHPLCAtpH7.5Cowan, HydrophobicityHPLCParkerAndOthers, HydrophobicityHPLCWilsonAndOthers, HydrophobicityHoppAndWoods, HydrophobicityJanin, HydrophobicityKyteAndDoolittle, HydrophobicityManavalanAndOthers, HydrophobicityMiyazawaAndOthers, HydrophobicityOMHSweetAndOthers, HydrophobicityRaoAndArgos, HydrophobicityRfMobility, HydrophobicityRoseAndOthers, HydrophobicityRoseman, HydrophobicityWellingAndOthers, HydrophobicityWolfendenAndOthers, ParallelBetaStrand, PolarityGrantham, PolarityZimmerman, RatioHeteroEndToSide, RecognitionFactors, Refractivity, RelativeMutability, TotalBetaStrand, LinearStructure, LinearStructureAtpH7.4

--propertieslisting ByGroup | Alphabetical

Specify how to list properties for amino acids: group by category or an alphabetical by property names. Possible values: ByGroup or Alphabetical. Default: ByGroup.

-q, --quote yes | no

Put quotes around column values in output text file. Possible values: yes or no. Default value: yes.

-r, --root rootname

New text file name is generated using the root: <Root>.<Ext>. File name is only used during File value of -o, --output option.

Default file name: AminoAcidInfo<mode>.<Ext>. The csv, and tsv <Ext> values are used for comma/semicolon, and tab delimited text files respectively.

-w, --workingdir dirname

Location of working directory. Default: current directory.

EXAMPLES

To list basic properties information for amino acid Ala, type:

% InfoAminoAcids.pl

To list all available properties information for amino acid Ala, type:

% InfoAminoAcids.pl --propertiesmode all

To list basic properties information for amino acids Ala, Arg, and Asp type:

% InfoAminoAcids.pl Ala Arg Asp
% InfoAminoAcids.pl A Arg "Aspartic acid"

To list all available properties information for amino acids Ala, Arg, and Asp type:

% InfoAminoAcids.pl --propertiesmode all Ala Arg Asp

To list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp type:

% InfoAminoAcids.pl --propertiesmode Categories --properties BasicAndHydrophobicity Ala Arg Asp

To list OneLetterCode, ThreeLetterCode, DNACodons, and MolecularWeight for amino acids Ala, Arg, and Asp type:

% InfoAminoAcids.pl --propertiesmode Names --properties OneLetterCode,ThreeLetterCode,DNACodons,MolecularWeight Ala Arg Asp

To alphabetically list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp in rows insetad of amino acid blocks with quotes around the values, type:

% InfoAminoAcids.pl --propertiesmode Categories --properties BasicAndHydrophobicity --propertieslisting alphabetical --outdelim comma --outputstyle AminoAcidRows --quote yes Ala Arg Asp

To alphabetically list basic and hydrophobicty properties information for amino acids Ala, Arg, and Asp in rows insetad of amino acid blocks with quotes around the values and write them into a file AminoAcidProperties.csv, type:

% InfoAminoAcids.pl --propertiesmode Categories --properties BasicAndHydrophobicity --propertieslisting alphabetical --outdelim comma --outputstyle AminoAcidRows --quote yes --output File -r AminoAcidProperties -o Ala Arg Asp

AUTHOR

Manish Sud

SEE ALSO

InfoNucleicAcids.plInfoPeriodicTableElements.pl

COPYRIGHT

Copyright (C) 2017 Manish Sud. All rights reserved.

This file is part of MayaChemTools.

MayaChemTools is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

 

 

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