twofeat European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/feature_tables.twofeat http://www.ebi.ac.uk/soaplab/emboss4/services/feature_tables.twofeat?wsdl Finds neighbouring pairs of features in sequences. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/twofeat.html twofeat Finds neighbouring pairs of features in sequences. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/twofeat.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 sequence_direct_data parameter but not both together. Parameter mandatory if the sequence_direct_data parameter has not been chosen. false String sequence_direct_data Type: string. Any valid sequence. Choose this parameter if you want to provide the 'sequence' value as string. 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 send Type: long. The last position to be used in the sequence. This is an optional parameter. false String sprotein Type: boolean. Is the sequence a protein? This is an optional parameter. false String snucleotide Type: boolean. Is the sequence a nucleotide? This is an optional parameter. false String sreverse Type: boolean. Use reverse complement of the nucleic acid sequence. This is an optional parameter. false String slower Type: boolean. Convert the sequence to lower case. This is an optional parameter. false String supper Type: boolean. Convert the sequence to UPPER case. This is an optional parameter. false String atype Type: string. By default every feature in the feature table is allowed. You can set this to be any feature type you wish to allow. 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 allow more than one type, separate their names with the character '|', eg: *UTR | intron. This is an optional parameter. Default value is "*". * false String btype Type: string. By default every feature in the feature table is allowed. You can set this to be any feature type you wish to allow. 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 allow more than one type, separate their names with the character '|', eg: *UTR | intron. This is an optional parameter. Default value is "*". * false String minrange Type: long. If this is greater or equal to 'maxrange', then no min or max range is specified. This is an optional parameter. The default value is 0. 0 false String maxrange Type: long. If this is less than or equal to 'minrange', then no min or max range is specified. This is an optional parameter. The default value is 0. 0 false String asource Type: string. By default any feature source in the feature table is allowed. You can set this to match any feature source you wish to allow. 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 allow more than one source, separate their names with the character '|', eg: gene* | embl. This is an optional parameter. The default value is "*". * false String asense Type: string. By default any feature sense is allowed. You can set this to match the required sense. The allowed values for this parameter are: 0 (Any sense)| + (Forward sense)| - (Reverse sense). This is an optional parameter. The default value is 0. 0 false String aminscore Type: float. If this is greater than or equal to the maximum score, then any score is allowed. This is an optional parameter. The default value is 0.0. 0.0 false String amaxscore Type: float. If this is less than or equal to the maximum score, then any score is permitted. This is an optional parameter. The default value is 0.0. 0.0 false String atag 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'. 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 allowed. You can set this to match any feature tag you wish to allow. The tag may be wildcarded by using '*'. If you wish to allow more than one tag, separate their names with the character '|', eg: gene | label. This is an optional parameter. The default value is "*" * false String avalue Type: string. Tag values are the values associated with a feature tag. Tags are the types of extra values that a feature may have. Only some of these 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 allowed. You can set this to match any feature tag value you wish to allow. The tag value may be wildcarded by using '*'. If you wish to allow more than one tag value, separate their names with the character '|', eg: pax* | 10. This is an optional parameter. The default value is "*". * false String bsource Type: string. By default any feature source in the feature table is allowed. You can set this to match any feature source you wish to allow. 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 allow more than one source, separate their names with the character '|', eg: gene* | embl. This is an optional parameter. The default value is "*". * false String bsense Type: string. By default any feature sense is allowed. You can set this to match the required sense. The allowed values for this parameter are: 0 (Any sense)| + (Forward sense)| - (Reverse sense). This is an optional parameter. The default value is 0. 0 String bminscore Type: float. If this is greater than or equal to the maximum score, then any score is allowed. This is an optional parameter. The default value is 0.0. 0.0 false String bmaxscore Type: float. If this is less than or equal to the maximum score, then any score is permitted. This is an optional parameter. The default value is 0.0 0.0 false String btag Type: string. 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'. 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 allowed. You can set this to match any feature tag you wish to allow. The tag may be wildcarded by using '*'. If you wish to allow more than one tag, separate their names with the character '|', eg: gene | label. This is an optional parameter. The default value is "*" * false String bvalue Type: string. Tag values are the values associated with a feature tag. Tags are the types of extra values that a feature may have. Only some of these 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 allowed. You can set this to match any feature tag value you wish to allow. The tag value may be wildcarded by using '*'. If you wish to allow more than one tag value, separate their names with the character '|', eg: pax* | 10. This is an optional parameter. The default value is "*". * false String overlap Type: string. This allows you to specify the allowed overlaps of the features A and B. You can allow any or no overlaps, specify that they must or must not overlap, that one must or must not be wholly enclosed within another feature. This is an optional parameter. The allowed values for this parameter are: A (Any) | O (Overlap required)| NO (No overlaps are allowed)| NW (Overlap required but not within)| AW (A must be all within B)| BW (B must be all within A). The default value is A. A false String rangetype Type: string. This allows you to specify the positions from which the allowed minimum or maximum distance between the features is measured. This is an optional parameter. The allowed values for this parameter are: N (From nearest ends)| L (From left ends)| R (From right ends)| F (From furthest ends). The default value is N. N false String sense Type: string. This allows you to specify the required sense that the two features must be on. This is ignored (always 'Any') when looking at protein sequence features. This is an optional parameter. The allowed values for this parameter are: A (Any sense)| S (Same sense)| O (Opposite sense). The default value is A. A false String order Type: string. This allows you to specify the required order of the two features. The order is measured from the start positions of the features. This criterion is always applied despite the specified overlap type required. This is an optional parameter. The allowed values for this parameter are: A (Any)| AB (Feature A then feature B)| BA (Feature B then feature A). The default value is A. A false String twoout Type: boolean. If you set this to be true, then the two features themselves will be written out. If it is left as false, then a single feature will be written out covering the two features you found. This is an optional parameter. The default value is 'N' for No. N false String typeout Type: string. If you have specified that the pairs of features that are found should be reported as one feature in the ouput, then you can specify the 'type' name of the new feature here. By default every feature in the feature table is allowed. If you specify an invalid feature type name, then the default name 'misc_feature' is used. This is an optional parameter. misc_feature false String 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 list of sequence features false String http://www.mygrid.org.uk/ontology#retrieving http://www.mygrid.org.uk/ontology#EMBL_nucleotide_sequence_database Soaplab service