siggen European Bioinformatics Institute http://www.ebi.ac.uk/ EBI http://www.ebi.ac.uk/soaplab/emboss4/services/protein_3d_structure.siggen http://www.ebi.ac.uk/soaplab/emboss4/services/protein_3d_structure.siggen?wsdl Generates a sparse protein signature from an alignment. Detailed info about this operation can be found at the following link: http://liv.bmc.uu.se/cgi-bin/emboss/help/siggen siggen <s:soaplabwsdl xmlns:s="http://org.embl.ebi.escience/xscufl/0.1alpha">http://www.ebi.ac.uk/soaplab/emboss4/services/protein_3d_structure.siggen</s:soaplabwsdl> Generates a sparse protein signature from an alignment. Detailed info about this operation can be found at the following link: http://liv.bmc.uu.se/cgi-bin/emboss/help/siggen algpath DAF files (domain alignment files). A 'domain alignment file' contains a sequence alignment of domains belonging to the same SCOP or CATH family (or other node in the structural hierarchies). The file is in DAF format (CLUSTAL-like) and is annotated with domain family classification information. This is a mandatory parameter. ./ IDL:omg.org/DsLSRAnalysis/StringList:1.0 mode Specifies the mode of signature generation. There are 3 modes for signatures generatation: (1) Use positions specified in alignment file. The alignment file must contain a line beginning with the text 'Positions' for each line of the alignment. (2) Use a scoring method. The alignment is scored and the signature of a specified sparsity is sampled from high scoring positions. (3): Generate a randomised signature. A signature of a specified sparsity is sampled at random from the alignment. This is an optional parameter. The default is 1 1 String wsiz Type: long. Specifies the window size. When a signature is aligned to a protein sequence, the permissible gaps between two signature positions is determined by the empirical gaps and the window size. This is an optional parameter. The default is 0 0 String conoption Specifies the structure-based scoring scheme. SIGGEN provides 2 structure-based scoring schemes(plus a combination method) that are used to score the input alignment. This is an optional parameter. The allowed values for this parameter are: 1(Number)| 2(Conservation)| 3(Number and conservation)| 4(None (structural data available))| 5(None (no structural data available))| The default is 5 5 String conpath CON files (contact files). A 'contact file' contains contact data for a protein or a domain from SCOP or CATH, in the CON format(EMBL-like). The contacts may be intra-chain residue-residue,inter-chain residue-residue or residue-ligand. This is a mandatory parameter. ./ byte[][] cpdbpath CCF files(clean coordinate files). A 'clean cordinate file'contains protein coordinate and derived data for a single PDB file('protein clean coordinate file') or a single domain from SCOP or CATH ('domain clean coordinate file'), in CCF format (EMBL-like). The files, generated by using PDBPARSE (PDB files) or DOMAINER(domains), contain 'cleaned-up' data that is self-consistent and error-corrected. Records for residue solvent accessibility and secondary structure are added to the file by using PDBPLUS. This is a mandatory parameter. ./ byte[][] seqoption This option specifies the sequence-based scoring scheme. SIGGEN provides 2 sequence-based scoring schemes that are used to score the input alignment. This is an optional parameter. The allowed values for this parameter are: 1(Substitution matrix)| 2(Residue class)| 3(None)|. The default is 3 3 String datafile_direct_data Substitution matrix to use. The substitution matrix is used by the sequence-based scoring schemes. This is an optional parameter the default is 'EBLOSUM62'. The parameters 'datafile_direct_data' and 'datafile_url' are mutually exclusive. String datafile_url URL of substitution matrix to use. The substitution matrix is used by the sequence-based scoring schemes. This is an optional parameter the default is 'EBLOSUM62'. The parameters 'datafile_direct_data' and 'datafile_url' are mutually exclusive. EBLOSUM62 String sparsity This option specifies the % sparsity of signature. The signature sparsity is a user-defined parameter that determines how many residues the final signature will contain, for example, if the average sequence length of the proteins in the alignment is 250 residues, then a signature of sparsity 10% (default value) will contain 25 key residues or signature positions, that correspond to the top 25% highest scoring alignment positions. This is an optional parameter. 10 String filtercon Type: boolean(Yes/No).This option specifies whether to disregard positions forming few contacts only during the selection of signature positions. This is an optional parameter. The default is 'No'. N String conthresh This option specifies the threshold contact number. This controls the selection of key positions for the structure-based scoring scheme (number of contacts). This is an optional parameter. The default is 10. 10 String filterpsim Type: boolean (true/false). Disregard alignment sites that were not aligned satisfactorily. This is an optional parameter. The default is 'true'. true String report A general report for the underlying analysis job. String detailed_status The exit code of the underlying analysis job, 0 means the job returned normally. String sigoutdir Returns a signature report. A 'signature report' contains a sparse sequence signature suitable for use with the SIGSCAN and SIGGEN services. http://www.mygrid.org.uk/ontology#structural_alignment_report byte[][] http://www.mygrid.org.uk/ontology#predicting Soaplab service