emowse European Bioinformatics Institute http://www.ebi.ac.uk/ EBI http://www.ebi.ac.uk/soaplab/emboss4/services/protein_composition.emowse http://www.ebi.ac.uk/soaplab/emboss4/services/protein_composition.emowse?wsdl Protein identification by massspectrometry. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/emowse.html emowse Protein identification by massspectrometry. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/emowse.html sequence_usa Type: string. Protein sequence. 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 sequence_direct_data parameter but not both together. Parameter mandatory if the sequence_direct_data parameter has not been chosen. String sequence_direct_data Type: string. Protein sequence. Choose this parameter if you want to provide the 'sequence' value as string (protein sequence). Parameter mandatory if the sequence_usa parameter hasn't been chosen. http://www.mygrid.org.uk/ontology#protein_sequence 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 infile_direct_data Peptide molecular weight values. Parameter mandatory if the 'infile_usa' parameter has not been chosen. Both parameters are mutually exclusive. An example of input can be found here: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/emowse.html#input.1 String infile_url URL of peptide molecular weight values. Parameter mandatory if the 'infile_direct_data' parameter has not been chosen. Both parameters are mutually exclusive. String weight Type: long. Whole sequence molecular weight. This is an optional parameter. The default is 0. 0 String aadata_direct_data Type: string. Amino acids properties and molecular weight. This is an optional parameter. The parameters 'aadata_direct_data' and 'aadata_url' are mutually exclusive. String aadata_url Type: string. URL of amino acids properties and molecular weight. This is an optional parameter. The parameters 'aadata_direct_data' and 'aadata_url' are mutually exclusive. Eamino.dat String frequencies_direct_data Amino acid frequencies data. This is an optional parameter. The parameters 'frequencies_direct_data' and 'frequencies_url' are mutually exclusive. String frequencies_url URL of amino acid frequencies data. This is an optional parameter. The parameters 'frequencies_direct_data' and 'frequencies_url' are mutually exclusive. Efreqs.dat String enzyme Type: string. Enzyme or reagent. This is an optional parameter. The allowed values for this parameter are: 1(Trypsin)| 2(Lys-C)| 3(Arg-C)| 4(Asp-N)| 5(V8-bicarb)| 6(V8-phosph)| 7(Chymotrypsin)| 8(CNBr)| The default is 1 1 String pcrange Type: long. Allowed whole sequence weight variability. This is an optional parameter. The default is 25. 25 String tolerance Type: float. Tolerance. This is an optional parameter. The default is 0.1. 0.1 String partials Type: float. Partials factor. This is an optional parameter. The default is 0.4 0.4 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 outfile Returns: -1-Specified search parameters includes all specified parameters such as digest reagent, specified error tolerance, etc... -2-Short 'hit' listing the top 50 scoring proteins are then listed in descending order, details include the sequence ID name and brief text identifiers. -3-Detailed 'hit' listing the top 50 entries are then listed in more detail. The first line includes the sequence ID name, the emowse search score (typically a few powers of 10), the 'hit' protein Mw and finally an 'accuracy' ratio calculated by dividing 'hits' by the total number of peptides used for the search. Line 2 is the protein text identifier. Subsequent lines list 'hit' and 'miss' peptides, with the appropriate start, end and corresponding sequences of correct peptide matches. 'miss' peptides are indicated by 'No match' at the start of the last line for that protein. Matching peptides marked with a '*' denote partially-cleaved fragments. For an example of output: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/emowse.html#output.1 http://www.mygrid.org.uk/ontology#protein_sequence String http://www.mygrid.org.uk/ontology#predicting Soaplab service