NAME

mmb_pcb_ub_es.pm - Library for mmb_pcb_ub_es services.

SYNOPSIS

Usage:

 my $obj = Object->new ('src_human','Uniprot');
 print $obj->toString;
 my $aaSeq = inb_bsc_es::getAminoAcidSequence(
        'input' => $obj
        ) -> {'sequence'};
 print $aaSeq->SequenceString;

refreshWSDL parameter:

All methods have an additional parameter 'refreshWSDL' used to refresh the service WSDL. Default value is "false".

 my $aaSeq = inb_bsc_es::getAminoAcidSequence(
        'input' => $obj,
	'refreshWSDL' => "true"
        ) -> {'sequence'};

See also runService.

DESCRIPTION

Library to run available services from mmb_pcb_ub_es.

METHODS

getAminoAcidSequenceFromPDB

Produces full amino acid sequence that corresponds to a PDB entry

 (sequence => AminoAcidSequence) = getAminoAcidSequenceFromPDB 
		(
			input => Object
		)

getHeaderFromPDB

Retrieves headers from a PDB entry in PDB format

 (structure => PDB__Text) = getHeaderFromPDB 
		(
			input => Object
		)

getStructureFromPDB

Retrieves structure from PDB (PDB format) from a PDB Id Allows to specify a single chain using the format XXXX_X.

 (structure => PDB__Text) = getStructureFromPDB 
		(
			input => Object
		)

parseAminoAcidSequenceFromPDBText

Extracts amino acid sequence that corresponds to structure in PDB

 (sequence => AminoAcidSequence) = parseAminoAcidSequenceFromPDBText 
		(
			inputPDB => PDB__Text
		)

parseFeatureAASequenceFromFSOLVText

					Parses a FSOLVText report into a FeatureAASequence (the feature is DPS DG)			

 (sequence => FeatureAASequence) = parseFeatureAASequenceFromFSOLVText 
		(
			solvation => FSOLV_Text
		)

parseFeatureAASequenceFromPMUTText

					Parses a PMUTText report into a FeatureAASequence. Value is patogenicity prediction			

 (sequence => FeatureAASequence) = parseFeatureAASequenceFromPMUTText 
		(
			HSReport => PMUT_Text
		)

parseGFFFromFeatureAASequence

					Converts a feature AA sequence into GFF			

 (sequence => GFF) = parseGFFFromFeatureAASequence 
		(
			sequence => FeatureAASequence
		)

parseMultipleAlignFromBLASTText

Produces a multiple alignment in FASTA format from Blast Hits.

 (sequence => FASTA_AA_multi) = parseMultipleAlignFromBLASTText 
		(
			BlastReport => BLAST__Text
		)

parsePropertySequenceFromFSOLVText

					Parses a FSOLVText report into a PropertySequence			(where N means NORMAL and O means OUTSIDE)			

 (sequence => PropertySequence) = parsePropertySequenceFromFSOLVText 
		(
			solvation => FSOLV_Text
		)

parsePropertySequenceFromPMUTText

					Parses a PMUTText report into a PropertySequence			(where N means NEUTRAL and H means HOT-SPOT)			

 (sequence => PropertySequence) = parsePropertySequenceFromPMUTText 
		(
			HSReport => PMUT_Text
		)

plotFeatureAASequence

					Returns a 2D graphic from a FeatureAASequence (png image)			

 (image => Typed_Image) = plotFeatureAASequence 
		(
			sequence => FeatureAASequence
		)

runFSOLVFromPDBText

					Evaluates fractional solvation based on LRT method			

 (solvation => FSOLV_Text) = runFSOLVFromPDBText 
		(
			structure => PDB__Text
		)

runPHDFromAminoAcidSequence

Performs secondary structure and accessibility predictions using PHD

 (PHDReport => PHD_Text) = runPHDFromAminoAcidSequence 
		(
			sequence => AminoAcidSequence
		)

runPHDFromBLASTText

Predicts secondary structure and accessibility using PHD program

 (PHDReport => PHD_Text) = runPHDFromBLASTText 
		(
			BlastReport => BLAST__Text
		)

runPHDFromFASTA

Performs secondary structure and accessibility predictions using PHD

 (PHDReport => PHD_Text) = runPHDFromFASTA 
		(
			sequence => FASTA_AA
		)

runPMUTHotSpotFromAminoAcidSequence

Predicts sequence positions (Hot Spots) that would produce pathological behaviour when mutated. Trained with human pathological mutations

 (HSReport => PMUT_Text) = runPMUTHotSpotFromAminoAcidSequence 
		(
			sequence => AminoAcidSequence
		)

runPMUTHotSpotFromBLASTText

Predicts sequence positions (Hot Spots) that would produce pathological behaviour when mutated. Trained with human pathological mutations

 (HSReport => PMUT_Text) = runPMUTHotSpotFromBLASTText 
		(
			BlastReport => BLAST__Text
		)

runPMUTHotSpotFromFASTA

Predicts sequence positions (Hot Spots) that would produce pathological behaviour when mutated. Trained with human pathological mutations

 (HSReport => PMUT_Text) = runPMUTHotSpotFromFASTA 
		(
			sequence => FASTA_AA
		)

runPSIBlastpFromAminoAcidSequence

Perform 2 iterations of protein PSI Blast against non-redundant database with standard settings

 (BlastReport => BLAST__Text) = runPSIBlastpFromAminoAcidSequence 
		(
			sequence => AminoAcidSequence
		)

runPSIBlastpFromFASTA

Perform 2 iterations of protein PSI Blast against non-redundant database with standard settings

 (BlastReport => BLAST__Text) = runPSIBlastpFromFASTA 
		(
			sequence => FASTA_AA
		)

showFSOLVonStructure

					FSolv report 3D representation			

 (structure => PDB_Enriched) = showFSOLVonStructure 
		(
			structure => PDB__Text,
			solvation => FSOLV_Text
		)

showPMUTonStructure

					PMUT report 3D representation			

 (structure => PDB_Enriched) = showPMUTonStructure 
		(
			structure => PDB__Text,
			HSReport => PMUT_Text
		)