showfeat European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/display.showfeat http://www.ebi.ac.uk/soaplab/emboss4/services/display.showfeat?wsdl It reads a protein or nucleic sequence and displays its features. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/showfeat.html showfeat It reads a protein or nucleic sequence and displays its features. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/showfeat.html sequence_usa Type: string. any valid 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 asequence_direct_data parameter but not both together. Parameter mandatory if the asequence_direct_data parameter hasn't been chosen. false String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter sequence_direct_data Type: string. Any valid sequence. Choose this parameter if you want to provide the 'sequence' value as string(nucleotide or protein sequence). Parameter mandatory if the sequence_usa parameter hasn't been chosen. false http://www.mygrid.org.uk/ontology#biological_sequence http://www.mygrid.org.uk/ontology#single_sequence_format String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter 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. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter sbegin Type: long. The first position to be used in the sequence, for example: sbegin=1 means start with the first base in the sequence. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter send Type: long. The last position to be used in the sequence. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter sprotein Type: boolean. Is the sequence a protein? This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter snucleotide Type: boolean. Is the sequence a nucleotide? This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter sreverse Type: boolean. Use reverse complement of the nucleic acid sequence. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter slower Type: boolean. Convert the sequence to lower case. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter supper Type: boolean. Convert the sequence to UPPER case. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter matchsource Type: string. By default any feature source in the feature table is shown. You can set this parameter to match any feature source you wish to show. The source name is usually either the name of the program that detected the feature or it is the feature table (eg: EMBL) that the feature came from. The source may be wildcarded by using '*'. If you wish to show more than one source, separate their names with the character '|'. For example: gene* | embl. This is an optional parameter. * false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter matchtype Type: string. By default any feature type in the feature table is shown. You can set this to match any feature type you wish to show. See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature types. The type may be wildcarded by using '*'. If you wish to show more than one type, separate their names with the character '|'. For example: *UTR | intron. This is an optional parameter. * false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter matchtag Type: string. Tags are the types of extra values that a feature may have. For example in the EMBL feature table, a 'CDS' type of feature may have the tags '/codon', '/codon_start', '/db_xref', '/EC_number', '/evidence', '/exception', '/function', '/gene', '/label', '/map', '/note', '/number', '/partial', '/product', '/protein_id', '/pseudo', '/standard_name', '/translation', '/transl_except', '/transl_table', or '/usedin'. Some of these tags also have values, for example '/gene' can have the value of the gene name. By default any feature tag in the feature table is shown. You can set this to match any feature tag you wish to show. The tag may be wildcarded by using '*'. If you wish to show more than one tag, separate their names with the character '|'. For example gene | label. This is an optional parameter. * false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter matchvalue Type: string. Tag values are the values associated with a feature tag. Only some tags can have values, for example '/gene' can have the value of the gene name. By default any feature tag value in the feature table is shown. You can set this to match any feature tag value you wish to show. The tag value may be wildcarded by using '*'. If you wish to show more than one tag value, separate their names with the character '|'. For example: pax* | 10. This is an optional parameter. * false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter sort Type: string. Sorting features. The allowed values for this parameter are: source (Sort by Source) | start (Sort by Start position) | type (Sort by Type) | nosort (No sorting done)| join (Join coding regions together) This is an optional parameter. The default value is "start". start false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter annotation Type: string. Regions to annotate by marking. If this is left blank, then no annotation is added. A set of regions is specified by a set of pairs of positions followed by optional text. The positions are integers. They are followed by any text. Examples of region specifications are: 24-45 new domain 56-78 match to Mouse 1-100 First part 120-156 oligo. A file of ranges to annotate (one range per line) can be specified as '@filename'. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter html Type: boolean. If you are sending the output to a file, this will format it for displaying as a table in a WWW document. False by default. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter id Type: boolean. Set this to be false if you do not wish to display the ID name of the sequence. True by default. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter description Type: boolean. Set this to be false if you do not wish to display the description of the sequence. True by default. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter scale Type: boolean. Set this to be false if you do not wish to display the scale line. True by default. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter width Type: long. You can expand (or contract) the width of the ASCII-character graphics display of the positions of the features using this value. For example, a width of 80 characters would cover a standard page width and a width of 10 characters would be nearly unreadable. If the width is set to less than 4, the graphics lines and the scale line will not be displayed. This is an optional parameter. The default value is 60. 60 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter collapse Type: boolean. If this is set, then features from the same source and of the same type and sense are all printed on the same line. For instance if there are several features from the EMBL feature table (ie. the same source) which are all of type 'exon' in the same sense, then they will all be displayed on the same line. This makes it hard to distinguish overlapping features. If this is set to false then each feature is displayed on a separate line making it easier to distinguish where features start and end. This is an optional parameter. False by default. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter forward Type: boolean. Set this to be false if you do not wish to display forward sense features. This is an optional parameter. True by default. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter reverse Type: boolean. Set this to be false if you do not wish to display reverse sense features. This is an optional parameter. True by default. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter unknown Type: boolean. Set this to be false if you do not wish to display unknown sense features. (ie. features with no directionality - all protein features are of this type and some nucleic features (for example,CG-rich regions)). This is an optional parameter. True by default. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter strand Type: boolean. Set this if you wish to display the strand of the features. Protein features are always directionless (indicated by '0'), forward is indicated by '+' and reverse is '-'. This is an optional parameter. False by default. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter source Type: boolean. Set this to true if you wish to display the source of the features. The source name is usually either the name of the program that detected the feature or it is the name of the feature table (eg:EMBL) that the feature came from. This is an optional parameter. False by default. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter position Type: boolean. Set this to true if you wish to display the start and end position of the features. If several features are being displayed on the same line, then the start and end positions will be joined by a comma, for example: '189-189,225-225'. This is an optional parameter. False by default. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter type Type: boolean. Set this to be false if you do not wish to display the type of the features. This is an optional parameter. True by default. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter tags Type: boolean. Set this to be false if you do not wish to display the tags and values of the features. This is an optional parameter. False by default. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter values Type: boolean. Set this to be false if you do not wish to display the tag values of the features. If this is set to be false, only the tag names will be displayed. If the tags are not displayed, then the values will not be displayed. The value of the 'translation' tag is never displayed as it is often extremely long. This is an optional parameter. True by default. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter stricttags Type: boolean. By default if any tag/value pair in a feature matches the specified tag and value, then all the tags/value pairs of that feature will be displayed. If this is set to be true, then only those tag/value pairs in a feature that match the specified tag and value will be displayed. This is an optional parameter. False by default. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter report Type: string. A general report for the underlying analysis job. false String detailed_status Type: long. The exit code of the underlying analysis job, 0 means the job returned normally. false String outfile Returns the features table of specified sequences. false http://www.mygrid.org.uk/ontology#nucleotide_sequence_feature_diagram String http://www.mygrid.org.uk/ontology#retrieving Soaplab service