NAME

inb_bsc_es.pm - Library for inb_bsc_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 inb_bsc_es.

METHODS

fromClustalwToPhylip

It converts a Clustalw data type into a Phylip Interleaved data type.

 (phylip_alignment => Phylip_Interleaved_Text) = fromClustalwToPhylip 
		(
			clustalw_alignment => Clustalw_Text
		)

getAminoAcidSequence

Retrieves an aminoacid sequence from an aminoacid database.

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

getEntryFromDSSP

Retrieves an entry from a DSSP database.

 (entry => DSSP_Text) = getEntryFromDSSP 
		(
			id => Object
		)

getEntryFromEMBL

Retrieves an entry from an EMBL database.

 (entry => EMBL_Text) = getEntryFromEMBL 
		(
			id => Object
		)

getEntryFromFSSP

Retrieves an entry from a FSSP database.

 (entry => FSSP_Text) = getEntryFromFSSP 
		(
			id => Object
		)

getEntryFromGenBank

Retrieves an entry from GenBank database.

 (entry => GenBank_Text) = getEntryFromGenBank 
		(
			id => Object
		)

getEntryFromHSSP

Retrieves an entry from a HSSP database.

 (entry => HSSP_Text) = getEntryFromHSSP 
		(
			id => Object
		)

getEntryFromPDB

Retrieves an entry from PDB database.

 (entry => PDB__Text) = getEntryFromPDB 
		(
			id => Object
		)

getEntryFromPfam

Gets a HMM from Pfam given an ACC identifier.

 (entry => HMM_Text) = getEntryFromPfam 
		(
			id => Object
		)

getEntryFromRefSeq

Retrieves an entry from RefSeq database.

 (entry => RefSeq_Text) = getEntryFromRefSeq 
		(
			id => Object
		)

getEntryFromSwissProt

Retrieves an entry from SwissProt database.

 (entry => SwissProt_Text) = getEntryFromSwissProt 
		(
			id => Object
		)

getEntryFromTrEMBL

Retrieves an entry from TrEMBL database.

 (entry => SwissProt_Text) = getEntryFromTrEMBL 
		(
			id => Object
		)

getEntryFromUniProt

Retrieves an entry from UniProt database.

 (entry => SwissProt_Text) = getEntryFromUniProt 
		(
			id => Object
		)

getFeatureAASequenceFromUniprot

Returns a sequence from uniprot annotated with all its features.

 (sequence => FeatureAnnotatedAASequence) = getFeatureAASequenceFromUniprot 
		(
			id => Object
		)

getNucleotideSequence

Retrieves a nucleotide sequence from a nucleotide database.

 (sequence => NucleotideSequence) = getNucleotideSequence 
		(
			input => Object
		)

runClustalwFast

ClustalW multiple sequence alignments (fast method).

 (clustalw_report => Clustalw_Text) = runClustalwFast 
		(
			sequences => [GenericSequence],
			gapopen => Float,
			endgaps => String,
			gapdist => Integer,
			pairgap => Integer,
			matrix => String,
			topdiag => Integer,
			window => Integer,
			transitions_weight => Float,
			gapext => Float,
			ktup => Integer
		)

runClustalwFull

ClustalW multiple sequence alignments (full method).

 (clustalw_report => Clustalw_Text) = runClustalwFull 
		(
			sequences => [GenericSequence],
			pwgapopen => Float,
			gapopen => Float,
			pwgapext => Float,
			gapdist => Integer,
			endgaps => String,
			matrix => String,
			gapext => Float,
			transitions_weight => Float,
			pwmatrix => String
		)

runEmbossNeedleFromSequences

Makes a pairwise global alingment using the Needleman-Wunsch global alignment algorithm.

 (pairwise_alignment => MSF) = runEmbossNeedleFromSequences 
		(
			sequence => GenericSequence,
			database => GenericSequence,
			gapextend => Float,
			datafile => String,
			gapopen => Float
		)

runEmbossPepinfoFromSequence

Pepinfo detects and displays various useful metrics about a protein sequence.

 (pepinfo_report => PepinfoReport) = runEmbossPepinfoFromSequence 
		(
			sequence => AminoAcidSequence,
			hwindow => Integer,
			to => Integer,
			from => Integer
		)

runFastaForAminoAcids

Compares a protein sequence against a protein database using the FASTA algorithm.

 (fasta_report => FASTA_Text) = runFastaForAminoAcids 
		(
			sequence => AminoAcidSequence,
			gap_open => Integer,
			alignments_number => Integer,
			high_scores_number => Integer,
			gap_extension => Integer,
			expectation_upper_value => Float,
			database => String,
			ktup => Integer,
			scoring_matrix => String
		)

runFastx

Compares a nucleotide sequence (it is translated with frameshifts) against a protein database using the FASTA (fastx) algorithm.

 (fasta_report => FASTA_Text) = runFastx 
		(
			sequence => NucleotideSequence,
			alignments_number => Integer,
			between_codon => Integer,
			high_scores_number => Integer,
			gap_extension => Integer,
			expectation_upper_value => Float,
			database => String,
			ktup => Integer,
			gap_open => Integer,
			scoring_matrix => String
		)

runFasty

Compares a nucleotide sequence (it is translated with frameshifts and it allows frameshifts inside codons) against a protein database using the FASTA (fasty) algorithm.

 (fasta_report => FASTA_Text) = runFasty 
		(
			sequence => NucleotideSequence,
			alignments_number => Integer,
			high_scores_number => Integer,
			database => String,
			gap_extension => Integer,
			expectation_upper_value => Float,
			ktup => Integer,
			within_codon => Integer,
			between_codon => Integer,
			gap_open => Integer,
			scoring_matrix => String
		)

runHMMBuild

 It constructs a Hidden Markov Model from a multiple sequence alignment.

 (profile => HMM_Text) = runHMMBuild 
		(
			alignment => Sequence_alignment_report,
			swentry => Float,
			fast_algorithm => String,
			architecture_prior => Float,
			weighting_algorithm => String,
			fast_construction => Float,
			idlevel => Float,
			pb_weights => Integer,
			alignment_method => String,
			swexit => Float
		)

runHMMPfam

Searches a HMM profile database (Pfam) with a query sequence. Use this if you are trying to annotate an unknown sequence.

 (hmmpfam_report => HMMPfam_Report) = runHMMPfam 
		(
			sequence => AminoAcidSequence,
			e__value_score => Integer,
			score_cutoff => Integer,
			alignment_number => Integer,
			e__value_domain => Float,
			hmm_accessions => String,
			score_cutoff_domain => Integer,
			e__value => Float
		)

runHMMSearchAgainstSeqs

Searches a set of sequences with a HMM profile.

 (hmmsearch_report => HMMSearch_Report) = runHMMSearchAgainstSeqs 
		(
			profile => HMM_Text,
			sequences => [GenericSequence],
			e__value_score => Integer,
			score_cutoff => Integer,
			alignment_number => Integer,
			e__value_domain => Float,
			score_cutoff_domain => Integer,
			e__value => Float
		)

runNCBIBlastn

Compares a nucleotide sequence to a nucleotide sequence database and calculates the statistical significance of matches using the Basic Local Alignment Search Tool (BLAST).

 (blast_report => BLAST__Text) = runNCBIBlastn 
		(
			sequence => NucleotideSequence,
			scores => Integer,
			dropoff => Integer,
			filter => String,
			extendgap => Integer,
			alignments => Integer,
			database => String,
			expect_threshold => Float,
			gapalign => String,
			opengap => Integer
		)

runNCBIBlastn_2Seqs

Compares a nucleotide sequence against another nucleotide sequence (used as a database) using the Basic Local Alignment Tool (BLAST).

 (bl2seq_report => BLAST__Text) = runNCBIBlastn_2Seqs 
		(
			database => NucleotideSequence,
			sequence => NucleotideSequence,
			gapalign => String,
			expect_threshold => Float,
			mismatch => Integer,
			match => Integer,
			word_size => Integer,
			extendgap => Integer,
			filter => String,
			dropoff => Integer,
			opengap => Integer
		)

runNCBIBlastp

Compares a protein sequence against a protein database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST).

 (blast_report => BLAST__Text) = runNCBIBlastp 
		(
			sequence => AminoAcidSequence,
			opengap => Integer,
			gapalign => String,
			extendGap => Integer,
			expect_threshold => Float,
			database => String,
			alignments => Integer,
			matrix => String,
			filter => String,
			dropoff => Integer,
			scores => Integer
		)

runNCBIBlastp_2Seqs

Compares a protein sequence against another protein sequence (used as a database) using the Basic Local Alignment Tool (BLAST).

 (bl2seq_report => BLAST__Text) = runNCBIBlastp_2Seqs 
		(
			database => AminoAcidSequence,
			sequence => AminoAcidSequence,
			opengap => Integer,
			matrix => String,
			gapalign => String,
			word_size => Integer,
			extendgap => Integer,
			filter => String,
			expect_threshold => Float,
			dropoff => Integer
		)

runNCBIBlastx

Compares a nucleotide query sequence translated in all reading frames against a protein sequence database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST).

 (blastx_report => BLAST__Text) = runNCBIBlastx 
		(
			sequence => NucleotideSequence,
			opengap => Integer,
			gapalign => String,
			expect_threshold => Float,
			alignments => Integer,
			matrix => String,
			database => String,
			extendgap => Integer,
			filter => String,
			dropoff => Integer,
			scores => Integer
		)

runNCBIBlastx_2Seqs

Compares a nucleotide query sequence translated in all reading frames against a protein sequence (used as a database) using the Basic Local Alignment Tool (BLAST).

 (bl2seq_report => BLAST__Text) = runNCBIBlastx_2Seqs 
		(
			sequence => NucleotideSequence,
			database => AminoAcidSequence,
			dropoff => Integer,
			expect_threshold => Float,
			filter => String,
			extendgap => Integer,
			word_size => Integer,
			gapalign => String,
			matrix => String,
			opengap => Integer
		)

runNCBITBlastn

Compares an amino acid sequence against the six-frame translations of a nucleotide sequence database and calculates the statistical significance of matches using the Basic Local Alignment Search Tool (BLAST).

 (blast_report => BLAST__Text) = runNCBITBlastn 
		(
			sequence => AminoAcidSequence,
			scores => Integer,
			dropoff => Integer,
			filter => String,
			extendgap => Integer,
			alignments => Integer,
			matrix => String,
			database => String,
			expect_threshold => Float,
			gapalign => String,
			opengap => Integer
		)

runNCBITBlastn_2Seqs

Compares a protein sequence against a nucleotide sequence (used as a database) dynamically translated in all six reading frames (both strands) using the Basic Local Alignment Tool (BLAST).

 (bl2seq_report => BLAST__Text) = runNCBITBlastn_2Seqs 
		(
			sequence => AminoAcidSequence,
			database => NucleotideSequence,
			dropoff => Integer,
			expect_threshold => Float,
			filter => String,
			extendgap => Integer,
			word_size => Integer,
			gapalign => String,
			matrix => String,
			opengap => Integer
		)

runNCBITBlastx

Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database and calculates the statistical significance of matches using the Basic Local Alignment Search Tool (BLAST).

 (blast_report => BLAST__Text) = runNCBITBlastx 
		(
			sequence => NucleotideSequence,
			scores => Integer,
			dropoff => Integer,
			filter => String,
			extendgap => Integer,
			alignments => Integer,
			matrix => String,
			database => String,
			expect_threshold => Float,
			gapalign => String,
			opengap => Integer
		)

runNCBITBlastx_2Seqs

Compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence (used as a database) using the Basic Local Alignment Tool (BLAST).

 (bl2seq_report => BLAST__Text) = runNCBITBlastx_2Seqs 
		(
			sequence => NucleotideSequence,
			database => NucleotideSequence,
			dropoff => Integer,
			expect_threshold => Float,
			filter => String,
			extendgap => Integer,
			word_size => Integer,
			gapalign => String,
			matrix => String,
			opengap => Integer
		)

runPhylipDnadist

Uses nucleotide sequences to compute a distance matrix, under four different models of nucleotide substitution.

 (matrix => Distance_Matrix) = runPhylipDnadist 
		(
			alignment => Phylip_Text,
			basefrequency => String,
			matrix => String,
			freqt => Float,
			freqc => Float,
			freqg => Float,
			freqa => Float,
			method => String,
			ttratio => Float
		)

runPhylipDnapars

Estimates phylogenies from nucleotide sequences by unrooted parsimony.

 (phylogenetic_tree => Newick_Text) = runPhylipDnapars 
		(
			alignment => Phylip_Text,
			randseed => Integer,
			random => String,
			threshold => Float,
			randtimes => Integer,
			outgroup_root => String,
			outgnum => Integer
		)

runPhylipProtdist

Uses protein sequences to compute a distance matrix, under three different models of aminoacid replacement.

 (matrix => Distance_Matrix) = runPhylipProtdist 
		(
			alignment => Phylip_Text,
			changeprob => Float,
			method => String,
			category => String,
			ttratio => Float,
			gencode => String
		)

runPhylipProtpars

Estimates phylogenies from protein sequences by unrooted parsimony.

 (phylogenetic_tree => Newick_Text) = runPhylipProtpars 
		(
			alignment => Phylip_Text,
			outgroup_root => String,
			randtimes => Integer,
			threshold => Float,
			random => String,
			randseed => Integer,
			outgnum => Integer
		)

runTcoffeeEvaluateAlignments

Evaluation of an alignment using Tcoffee.

 (tcoffee_evaluation => Clustalw_Evaluated_Text) = runTcoffeeEvaluateAlignments 
		(
			alignment => Clustalw_Text
		)

runTcoffeeFromProfiles

Makes a profile alignment using Tcoffee.

 (tcoffee_report => Clustalw_Text) = runTcoffeeFromProfiles 
		(
			alignments => [Clustalw_Text],
			profile_mode => String,
			clustalw_header => String,
			profile_comparison => String
		)

runTcoffeeFromSequences

Multiple sequence alignment usinf T-coffee.

 (tcoffee_report => Clustalw_Text) = runTcoffeeFromSequences 
		(
			sequences => [GenericSequence],
			gapopen => Integer,
			method => String,
			ndiag => Integer,
			tree_mode => String,
			ktuple => Integer,
			dp_mode => String,
			do_normalise => Integer,
			extend_mode => String,
			diag_mode => Integer,
			clustalw_header => String,
			gapext => Integer,
			extend => Integer
		)

runWUBlastn_2Seqs

It compares a nucleotide query sequence against another nucleotide sequence (used as a database) using the Washington University BLAST algorithm.

 (wublastn_report => BLAST__Text) = runWUBlastn_2Seqs 
		(
			database => NucleotideSequence,
			sequence => NucleotideSequence,
			scores => Integer,
			gap_extension => Integer,
			expected_threshold => Float,
			filter => String,
			statistics => String,
			word_size => Integer,
			match => Integer,
			alignments => Integer,
			mismatch => Integer,
			nogaps => String,
			gap_open => Integer
		)

runWUBlastp

It compares an amino acid query sequence against a protein sequence database using the Washington University BLAST algorithm.

 (wublast_report => BLAST__Text) = runWUBlastp 
		(
			sequence => AminoAcidSequence,
			database => String,
			nogaps => String,
			matrix => String,
			alignments => Integer,
			scores => Integer,
			gap_extension => Integer,
			expected_threshold => Float,
			filter => String,
			statistics => String,
			word_size => Integer,
			gap_open => Integer
		)

runWUBlastp_2Seqs

It compares a protein sequence against another protein sequence (used as a database) using the Washington University BLAST algorithm.

 (wublastp_report => BLAST__Text) = runWUBlastp_2Seqs 
		(
			sequence => AminoAcidSequence,
			database => AminoAcidSequence,
			expected_threshold => Float,
			filter => String,
			statistics => String,
			word_size => Integer,
			alignments => Integer,
			matrix => String,
			gap_extension => Integer,
			scores => Integer,
			nogaps => String,
			gap_open => Integer
		)

runWUBlastx

It compares an amino acid query sequence against a protein sequence database using the Washington University BLAST algorithm.

 (wublast_report => BLAST__Text) = runWUBlastx 
		(
			sequence => NucleotideSequence,
			gap_open => Integer,
			nogaps => String,
			database => String,
			alignments => Integer,
			matrix => String,
			statistics => String,
			word_size => Integer,
			filter => String,
			expected_threshold => Float,
			gap_extension => Integer,
			scores => Integer
		)

runWUBlastx_2Seqs

It compares a nucleotide query sequence translated in all reading frames against a protein sequence (used as a database) using the Washington University BLAST algorithm.

 (wublastx_report => BLAST__Text) = runWUBlastx_2Seqs 
		(
			sequence => NucleotideSequence,
			database => AminoAcidSequence,
			scores => Integer,
			gap_extension => Integer,
			expected_threshold => Float,
			filter => String,
			statistics => String,
			word_size => Integer,
			alignments => Integer,
			matrix => String,
			nogaps => String,
			gap_open => Integer
		)

runWUTBlastn_2Seqs

It compares a protein sequence against a nucleotide sequence (used as a database) dynamically translated in all six reading frames (both strands) using the Washington University BLAST algorithm.

 (wutblastn_report => BLAST__Text) = runWUTBlastn_2Seqs 
		(
			sequence => AminoAcidSequence,
			database => NucleotideSequence,
			scores => Integer,
			gap_extension => Integer,
			expected_threshold => Float,
			filter => String,
			statistics => String,
			word_size => Integer,
			alignments => Integer,
			matrix => String,
			nogaps => String,
			gap_open => Integer
		)

runWUTBlastx_2Seqs

It compares a nucleotide query sequence against another nucleotide sequence (used as a database) using the Washington University BLAST algorithm.

 (wutblastx_report => BLAST__Text) = runWUTBlastx_2Seqs 
		(
			database => NucleotideSequence,
			sequence => NucleotideSequence,
			expected_threshold => Float,
			filter => String,
			statistics => String,
			word_size => Integer,
			alignments => Integer,
			matrix => String,
			nogaps => String,
			gap_extension => Integer,
			scores => Integer,
			gap_open => Integer
		)