sigscan European Bioinformatics Institute http://www.ebi.ac.uk/ EBI http://www.ebi.ac.uk/soaplab/emboss4/services/protein_3d_structure.sigscan http://www.ebi.ac.uk/soaplab/emboss4/services/protein_3d_structure.sigscan?wsdl Scans a signature (such as that generated by the EMBOSS application siggen) against swissprot database and writes a signature hits files. Detailed info about this operation can be found at the following link: http://liv.bmc.uu.se/cgi-bin/emboss/help/sigscan sigscan Scans a signature (such as that generated by the EMBOSS application siggen) against swissprot database and writes a signature hits files. Detailed info about this operation can be found at the following link: http://liv.bmc.uu.se/cgi-bin/emboss/help/sigscan dbsequence_usa Type: string. Protein sequence alignment. The Uniform Sequence Address, or USA, is a standard way of specifying a sequence to be read into a program in EMBOSS. The most common ways of specifying a sequence is to type (database:entry), where database can be embl, uniprot or swissprot and entry is either the sequence`s entry or ID name, or its Accession number in that database. For example:database:accession -->embl:X65923 or swissprot:Q7M4G0 | database:entry_name -->swissprot:AMIC_PSEAE |database:ID_name -->embl:paamir. Choose either this parameter or the dbsequence_direct_data parameter but not both together. Parameter mandatory if the dbsequence_direct_data parameter has not been chosen. String dbsequence_direct_data Type: string. Protein sequence alignment. Choose this parameter if you want to provide the 'dbsequence' value as string. Parameter mandatory if the dbsequence_usa parameter hasn't been chosen. An example of input can be found here: http://liv.bmc.uu.se/cgi-bin/emboss/help/sigscan#2.0 String sformat Type: string. Specifies the format of the input sequence. This is an optional parameter. The allowed values for this parameter are: gcg, gcg8, embl, swiss, fasta, ncbi, genbank, nbrf, pir, codata, strider, clustal, phylip, acedb, msf, jackknifer, jackknifernon, nexus, nexusnon, treecon, mega, meganon, ig, staden, text, raw. String sbegin Type: long. The first position to be used in the sequence, for example: sbegin=1 (default value) means start with the first base in the sequence. This is an optional parameter. String send Type: long. The last position to be used in the sequence. This is an optional parameter. By default it is the end of the sequence. String sprotein Type: boolean. Is the sequence a protein? This is an optional parameter. By default the service can autodetect if a sequence is a nucleotide or protein sequence. String snucleotide Type: boolean. Is the sequence a nucleotide? This is an optional parameter. By default the service can autodetect if a sequence is a nucleotide or protein sequence. String sreverse Type: boolean. Use reverse complement of the nucleic acid sequence. This is an optional parameter. False by default. String slower Type: boolean. Convert the sequence to lower case. This is an optional parameter. False by default. String supper Type: boolean. Convert the sequence to UPPER case. This is an optional parameter. False by default. String siginfile_direct_data Type: string. Signature file, it contains a sparse sequence signature. The files can be generated by using Emboss service SIGGEN. This is a mandatory parameter if the parameter 'siginfile_url' is not chosen. Both parameter are mutually exclusive. An example of input can be found here: http://liv.bmc.uu.se/cgi-bin/emboss/help/sigscan#2.0 String siginfile_url Type: string. URL of Signature file, it contains a sparse sequence signature. The files can be generated by using Emboss service SIGGEN. This is a mandatory parameter if the parameter 'siginfile_direct_data' is not chosen. Both parameter are mutually exclusive. String sub_direct_data Type: string. Residue substitution matrix. This is an optional parameter. The default is 'EBLOSUM62'. The parameters 'sub_direct_data' and 'sub_url' are mutually exclusive. String sub_url Type: string. URL of residue substitution matrix. This is an optional parameter. The parameters 'sub_direct_data' and 'sub_url' are mutually exclusive. The default is 'EBLOSUM62'. EBLOSUM62 String gapo Type: float. The gap insertion penalty is the score taken away when a gap is created. The best value depends on the choice of comparison matrix. The default value assumes you are using the EBLOSUM62 matrix for protein sequences, and the EDNAMAT matrix for nucleotide sequences. This is an optional parameter. Allowed value: floating point number from 1.0 to 100.0. The default is 10.0 10.0 String gape Type: float. The gap extension, penalty is added to the standard gap penalty for each base or residue in the gap. This is how long gaps are penalized. Usually you will expect a few long gaps rather than many short gaps, so the gap extension penalty should be lower than the gap penalty. An exception is where one or both sequences are single reads with possible sequencing errors in which case you would expect many single base gaps. You can get this result by setting the gap open penalty to zero (or very low) and using the gap extension penalty to control gap scoring. This is an optional parameter. Allowed value: floating point number from 0.0 to 10.0. The default is 0.5. 0.5 String nterm Type: string. This parameter specifies the N-terminal matching option. This determines how the first signature position is aligned to a sequence from the database. This is an optional parameter. The allowed values for this parameter are: 1(Align anywhere and allow only complete signature-sequence fit)| 2(Align anywhere and allow partial signature-sequence fit)| 3(Use empirical gaps only)| The default is 1 1 String nhits Type: long. Maximum number of hits to output. This is an optional parameter. The default is 100 100 String report Type: string. A general report for the underlying analysis job. String detailed_status Type: long. The exit code of the underlying analysis job, 0 means the job returned normally. String hitsfile Returns a domain hits report. A 'domain hits report' contains database hits(sequences) with domain classification information, in the DHF (Domain hits file) format (FASTA-like). The hits are relatives to a SCOP or CATH family (or other node in the structural hierarchies) and are found from a search of a sequence database. String alignfile Returns a signature alignment report. A 'signature alignment report' contains one or more signature-sequence alignments. The file is in DAF format(CLUSTAL-like) and is annotated with bibliographic information. http://www.mygrid.org.uk/ontology#structural_alignment_report String http://www.mygrid.org.uk/ontology#searching http://www.mygrid.org.uk/ontology#pattern_and_profile_search_algorithms Soaplab service