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Services marked with an 'A' can be executed in Altix Shared Memory computer.

Bioinformatics
Alignment
runEmbossConsFromAlignment	Creates a consensus from multiple alignments.
runNCBIFormatdb A	Formats a database into NCBI BLAST format.
Alignment > Multiple_Sequence_Comparison
runClustalwFast A	ClustalW multiple sequence alignments (fast method).
runClustalwFull A	ClustalW multiple sequence alignments (full method).
runMuscleFromSequences A	Muscle multiple sequence alignment.
runTcoffeeEvaluateAlignments A	Evaluation of an alignment using Tcoffee.
runTcoffeeFromProfiles A	Makes a profile alignment using Tcoffee.
runTcoffeeFromSequences A	Multiple sequence alignment usinf T-coffee.
Alignment > Pairwise_Sequence_Comparison > Pairwise_Local_Aligning
runBlat A	BLAT on DNA is designed to quickly find sequences of 95% and greater similarity of length 40 bases or more.
runFastaForAminoAcids A	Compares a protein sequence against a protein database using the FASTA algorithm.
runFastaForNucleotides A	Compares a nucleotide sequence against a nucleotide database using the FASTA algorithm.
runFastx A	Compares a nucleotide sequence (it is translated with frameshifts) against a protein database using the FASTA (fastx) algorithm.
runFasty A	Compares a nucleotide sequence (it is translated with frameshifts and it allows frameshifts inside codons) against a protein database using the FASTA (fasty) algorithm.
runNCBIBlastAgainstDB A	Compares a protein or dna sequence against a protein or dna database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST).
runNCBIBlastn A	Compares a nucleotide sequence to a nucleotide sequence database and calculates the statistical significance of matches using the Basic Local Alignment Search Tool (BLAST).
runNCBIBlastn_2Seqs A	Compares a nucleotide sequence against another nucleotide sequence (used as a database) using the Basic Local Alignment Tool (BLAST).
runNCBIBlastp A	Compares a protein sequence against a protein database and calculates the statistical significance of matches using the Basic Local Alignment Tool (BLAST).
runNCBIBlastp_2Seqs A	Compares a protein sequence against another protein sequence (used as a database) using the Basic Local Alignment Tool (BLAST).
runNCBIBlastx A	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).
runNCBIBlastx_2Seqs A	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).
runNCBITBlastn A	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).
runNCBITBlastn_2Seqs A	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).
runNCBITBlastx A	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).
runNCBITBlastx_2Seqs A	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).
runPSIBlast A	Compares a protein sequence to a sequence database and calculates the statistical significance of matches using the Position Specific Iterative BLAST (PSI-BLAST).
runPSIBlastXML A	Compares a protein sequence to a sequence database and calculates the statistical significance of matches using the Position Specific Iterative BLAST (PSI-BLAST).
runTFastx A	Compares a protein sequence against a nucleotide database translated in three forward and three reverse frames using the FASTA (tfastx) algorithm.
runTFasty A	Compares a protein sequence against a nucleotide database translated in three forward and three reverse frames using the FASTA (tfasty) algorithm. It allows frameshifts inside codons.
runWUBlastn A	It compares a nucleotide query sequence against a nucleotide sequence database using the Washington University BLAST algorithm.
runWUBlastn_2Seqs A	It compares a nucleotide query sequence against another nucleotide sequence (used as a database) using the Washington University BLAST algorithm.
runWUBlastp A	It compares an amino acid query sequence against a protein sequence database using the Washington University BLAST algorithm.
runWUBlastp_2Seqs A	It compares a protein sequence against another protein sequence (used as a database) using the Washington University BLAST algorithm.
runWUBlastx A	It compares an amino acid query sequence against a protein sequence database using the Washington University BLAST algorithm.
runWUBlastx_2Seqs A	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.
runWUTBlastn A	It compares an amino acid query sequence against the six-frame translations of a nucleotide sequence database using the Washington University BLAST algorithm.
runWUTBlastn_2Seqs A	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.
runWUTBlastx A	It compares the six-frame translations of a nucleotide query sequence against the six-frame translations of a nucleotide sequence database using the Washington University BLAST algorithm.
runWUTBlastx_2Seqs A	It compares a nucleotide query sequence against another nucleotide sequence (used as a database) using the Washington University BLAST algorithm.
Alignment > Profiling
runHMMBuild A	It constructs a Hidden Markov Model from a multiple sequence alignment.
runHMMPfam A	Searches a HMM profile database (Pfam) with a query sequence. Use this if you are trying to annotate an unknown sequence.
runHMMSearchAgainstDB A	Searches a sequence database with a HMM profile.
runHMMSearchAgainstSeqs A	Searches a set of sequences with a HMM profile.
runRPSBlast A	RPS-BLAST (Reverse PSI-BLAST) searches a query sequence against a database of profiles.
Alignment > Single_Sequence_Comparison > Pairwise_2Global_Aligning
runEmbossNeedleFromSequences A	Makes a pairwise global alingment using the Needleman-Wunsch global alignment algorithm.
Alignment > Single_Sequence_Comparison > Pairwise_2Local_Aligning
runEmbossWaterFromSequences A	Makes a pairwise global alingment using the Needleman-Wunsch global alignment algorithm.
Biochemestry > EnzymeKinetics
runEmbossFindkm A	Finds the Michaelis Menten constant (Km) and the maximum velocity (Vmax) for an enzyme reaction by a Michaelis Menten and Hanes/Woolf plot.
Database > Retrieving > GettingSequences > GettingAminoacids
getAminoAcidSequence	Retrieves an aminoacid sequence from an aminoacid database.
getFeatureAASequenceFromUniprot	Returns a sequence from uniprot annotated with all its features.
Database > Retrieving > GettingSequences > GettingNucleotides
getCDSSequence	Extract CDS sequences.
getNucleotideSequence	Retrieves a nucleotide sequence from a nucleotide database.
getSequenceByRegionFromENSEMBL	Retrieves an ENSEMBL sequence by its region.
getSequencesFromENSEMBLHomology	Retrieves all sequence of an ENSEMBL homology.
Database > Retrieving > GettingStructures
getAtomsFromPDBID	Retrieves an entry from PDB database.
getEntryFromPDB	Retrieves an entry from PDB database.
Database > Retrieving > GettingText
fromPDBTextToDSSP	Retrieves an entry from a DSSP database.
getCodonTableFromEmboss	This is a utility to indicate which directories can hold EMBOSS data files and what the names of these files are
getDocumentationFromProsite	Retrieves a documentation file from prosite.
getEntryFromDSSP	Retrieves an entry from a DSSP database.
getEntryFromEMBL	Retrieves an entry from an EMBL database.
getEntryFromFSSP	Retrieves an entry from a FSSP database.
getEntryFromGenBank	Retrieves an entry from GenBank database.
getEntryFromHSSP	Retrieves an entry from a HSSP database.
getEntryFromOMIM	Retrieves an entry from OMIM, Online Mendelian Inheritance in Man, database.
getEntryFromPfam	Gets a HMM from Pfam given an ACC identifier.
getEntryFromProdom	It extracts a ProDom entry (query by accession number).
getEntryFromProsite	Retrieves a motif from prosite.
getEntryFromRefSeq	Retrieves an entry from RefSeq database.
getEntryFromSwissProt	Retrieves an entry from SwissProt database.
getEntryFromTrEMBL	Retrieves an entry from TrEMBL database.
getEntryFromUniProt	Retrieves an entry from UniProt database.
getGOTerm	Retrieves a GO Term from the Gene Ontology database.
getmmCifFileFromPDBID	Gets the contents of a file in format mmCIF from PDB given an PDBID.
Database > Retrieving
browseCATHClassification	Browse cath hierarchical classification. Given a node number, this service returns all its children.
getCATHHierarchyCodesFromPDBID	Retrieves all domain hierarchy codes from a pdb id.
getEnsemblIDsFromUniprot	Returns Ensembl cross references from an uniprot entry.
getEntryFromCATH	Retrieves a domain entry from CATH.
getEntryFromSCOPDomainID	Retrieves a domain entry from SCOP database.
getEntryFromSCOPPath	Retrieves a hierarchical non domain entry from SCOP database.
getGraphFromTerm	Retrieves the Gene Ontology graph from a term.
getHSSPIDsFromUniprot	Returns pdb cross references from an uniprot entry.
getHomologiesFromEnsembl	Retrieves homologies from ENSEMBL.
getPDBIDsFromUniprot	Returns pdb cross references from an uniprot entry.
getTermsFromProduct	Retrieves GO Terms related to a product.
getUniprotAccessionsFromID	Returns all accessions of a Uniprot entry identified by the input id.
getUniprotIDsFromAccession	Returns the names or ids of a uniprot entry identified by the input accession.
getUniprotIDsFromGOTerm	Get Uniprot IDs related to a GO Term.
Database > Searching
getCATHDomainsFromPDBID	Returns the domains and fragments of a pdb id.
refineTextQueryOMIM	Searches a text in OMIM records (more precisely, the text is searched in these fields: text, allelicvariants, clinical synopsis and references).
textQueryOMIM	Searches a text in OMIM records (more precisely, the text is searched in these fields: text, allelicvariants, clinical synopsis and references).
textQueryUniprot	Searches uniprot entries for a text. The text is searched in: comments and keywords.
Distances > Phylogenetics > Distance_Matrix_Computing
runPhylipDnadist A	Uses nucleotide sequences to compute a distance matrix, under four different models of nucleotide substitution.
runPhylipProtdist A	Uses protein sequences to compute a distance matrix, under three different models of aminoacid replacement.
Distances > Phylogenetics > Phylogenetics_Tree_Computing
runPhylipDnaml A	Estimates phylogenies from nucleotide sequences by maximum likelihood.
runPhylipDnamlk A	Estimates phylogenies from nucleotide sequences by maximum likelihood under the constraint that the trees estimated must be consistent with a molecular clock.
runPhylipDnapars A	Estimates phylogenies from nucleotide sequences by unrooted parsimony.
runPhylipDnapenny A	Estimates phylogenies from nucleotide sequences by branch and bound method.
runPhylipFitch A	Estimates phylogenies from distance matrix data using the Fitch-Margoliash method and some related least squares methods.
runPhylipKitsch A	Carries out the Fitch-Margoliash and Least-Squares methods, plus a variety of others of the same family, with the assumption that all tip species are contemporaneous, and there is an evolutionary clock.
runPhylipNeighbor A	Estimates phylogenies from distance matrix data using the Neighbor-Joining method or the UPGMA method of clustering.
runPhylipProtpars A	Estimates phylogenies from protein sequences by unrooted parsimony.
StructuralStudies > PhysicoChemical_Properties
runEmbossAntigenicFromSequence A	Antigenic predicts potentially antigenic regions of a protein sequence, using the method of Kolaskar and Tongaonkar.
runEmbossChargeFromSequence A	Reads a protein sequence and calculates the charges of the amino acids within a window of specified length.
runEmbossIepFromSequence A	It calculates the isoelectric point of a protein from its amino acid composition assuming that no electrostatic interactions change the propensity for ionization.
runEmbossOctanolFromSequence A	Displays protein hydropathy.
runEmbossPepinfoFromSequence A	Pepinfo detects and displays various useful metrics about a protein sequence.
runEmbossPepwindowFromSequence A	Pepwindow produces a graph of the classic Kyte and Doolittle hydropathy plot of a protein.
runEmbossPepwindowallFromSequences A	Pepwindowall produces a set of superimposed Kyte and Doolittle hydropathy plots from an aligned set of protein sequences.
runProCheckFromPDBText	Given a PDB file returns a PROCHECK analysis of such input.
SequenceAnalysis
runEmbossDigestFromSequence A	Digest finds the positions where a specified proteolytic enzyme or reagent might cut a peptide sequence.
runEmbossEmowse A	Search a protein database for matches with the mass spectrometry data.
runEmbossSigcleaveFromSequence A	Predicts the site of cleavage between a signal sequence and the mature exported protein.
runEmbossTmapFromSequence A	Displays membrane spanning regions.
runGenewise A	compares a protein sequence to a genomic DNA sequence, allowing for introns and frameshifting errors.
SequenceAnalysis > Composition
runEmbossCodcmpFromTables	This program compares two codon usage tables.
runEmbossCuspFromSequence A	Reads a CDS sequence and calculates a codon frequency table.
runEmbossPepstatsFromSequence A	Outputs a report of simple protein sequence information.
SequenceAnalysis > Nucleotic_Motifs
SequenceAnalysis > Protein_Motifs
getProdomDomainsFromUniProt	Return the decomposition in domains of a protein.
getPrositeAnnStructure	Annotates the prosite motifs of a structure.
getPrositeAnnStructureFromPDBID	Annotates the prosite motifs of a pdb entry.
runEmbossPatmatdb A	Takes a protein motif and compares it to a protein sequences.
runEmbossPatmatdbFromSequence A	Takes a protein motif and compares it to a protein sequences.
runEmbossPatmatmotifsFromSequence A	Patmatmotifs takes a protein sequence and compares it to the PROSITE database of motifs.
runPPSearchAgainstProsite A	Search your query sequence for protein motifs, rapidly compare your query protein sequence against all patterns stored in the PROSITE pattern database.
runPratt A	Search for patterns conserved in a set of protein sequences.
runPs_scanAgainstProsite A	Scan a protein sequence for the occurrence of patterns and profiles storedin the PROSITE database.
runPs_scanAgainstSequence A	Scan a protein sequence for the occurrence of a pattern.
searchBLOCKS A	It scans the entries from the Blocks databank against a protein sequence.
searchInterPro A	Query an Amino Acid sequence against InterPro.
StructuralStudies > Protein_Secondary_Structures
runEmbossPepcoilFromSequence A	Coiled coil region prediction.
SequenceAnalysis > Repetitions
runEmbossEquicktandemFromSequence A	Equicktandem scans a sequence for potential tandem repeats up to a specified size The results can be used to run etandem on the
SequenceAnalysis > Restrictions
runEmbossRestrictFromSequence A	Scans a nucleotide sequence for regions with higher than expected frequencies of the dinucleotide CG.
Translating
runEmbossGetorfFromSequence A	This program finds and outputs the sequences of open reading frames ORFs
runEmbossTranseqFromSequence A	Transeq translates nucleic acid sequences to the corresponding peptide sequences.
ObjectHandling
loadPersistentFile	Loads a persistent object and returns its reference.
getPersistentFile	Returns the value of a persistent object reference.
Converting
fromClustalwToPhylip	It converts a Clustalw data type into a Phylip Interleaved data type.
fromFastaToCommentedAASequence	Converts a sequence in Fasta format into a CommentedAASequence object.
fromFastaToCommentedNASequence	Converts a sequence in Fasta format into a CommentedNASequence object.
fromFastaToGenericSequence	Converts a sequence in Fasta format into a GenericSequence object.
fromGenericSequenceToFasta	Converts a GenericSequence object into a Fasta object.
fromGenericToAminoAcidSequence	Converts a GenericSequence object into an AminoAcidSequence.
fromGenericToNucleotideSequence	Converts a GenericSequence object into a NucleotideSequence.
fromNDBTextToPDBText	Translates a NDB-Text format to a PDB-Text format.
fromPDBTextToNDBText	Translate a PDB text format to NDB text format.
fromPDBTextTommCIF	Converts its input in PDB format to mmCIF format.
fromXYDataTextToArrayFloat	Get a molecular weight array from plain text (one weight per line).
Parsing
parseENSEMBLSliceInformation	Parses slice information of an ENSEMBL homolog.
parseFeatureAASequenceWithArticle	Parses the FeatureeAASequence having the input article.
parseMWfromMWAnnotatedAASequence	Parses a molecular weight array.
parseMatrixFromMotif	Parse a matrix from a motif.
parsePatternFromMotif	Parse a pattern from a motif.
parseRulesFromMotif	Parse rules from a motif.
runBlast2gene A	Analysis of genomic regions containing completely or partially duplicated genes: it all high scoring pairwise alignments (HSPs) and provides the disposition of all independent copies along the genomic fragment from a BLAST report.
Displaying
displayDomainsFromAnnStructure	Displays all domains of an annotated structural entry in different colors (using jmol script).
multiplotArrayXYData	Plots a collection of ArrayXYData
plotArrayXYData	Plots an ArrayXYData.