extractfeat European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/edit.extractfeat http://www.ebi.ac.uk/soaplab/emboss4/services/edit.extractfeat?wsdl Extract features from a sequence. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.1/emboss/apps/extractfeat.html extractfeat Extract features from a sequence. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.1/emboss/apps/extractfeat.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. 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 before Type: long. If this value is greater than 0 then that number of bases or residues before the feature are included in the extracted sequence. This allows you to get the context of the feature. If this value is negative then the start of the extracted sequence will be this number of bases/residues before the end of the feature. So a value of '10' will start the extraction 10 bases/residues before the start of the sequence, and a value of '-10' will start the extraction 10 bases/residues before the end of the feature. The output sequence will be padded with 'N' or 'X' characters if the sequence starts after the required start of the extraction. The default value is 0. This is an optional parameter. 0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter after Type: long. If this value is greater than 0 then that number of bases or residues after the feature are included in the extracted sequence. This allows you to get the context of the feature. If this value is negative then the end of the extracted sequence will be this number of bases/residues after the start of the feature. So a value of '10' will end the extraction 10 bases/residues after the end of the sequence, and a value of '-10' will end the extraction 10 bases/residues after the start of the feature. The output sequence will be padded with 'N' or 'X' characters if the sequence ends before the required end of the extraction. The default value is 0. This is an optional parameter. 0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter source Type: string. By default any feature source in the feature table is shown. You can set this 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 '|', eg: gene* | embl. This is an optional parameter. * false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter type Type: string. By default every feature in the feature table is extracted. You can set this to be any feature type you wish to extract. See http://www3.ebi.ac.uk/Services/WebFeat/ for a list of the EMBL feature type. The type may be wildcarded by using '*'. If you wish to extract more than one type, separate their names with the character '|', eg:*UTR | intron. This is an optional parameter. * false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter sense Type: long. By default any feature type in the feature table is extracted. You can set this to match any feature sense you wish. 0 for any sense, 1 for forward sense, -1 for reverse sense. The default value is 0. This is an optional parameter. 0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter minscore Type: float. Minimum score of feature to extract. If this is greater than or equal to the maximum score, then any score is permitted. Default value is 0.0. This is an optional parameter. 0.0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter maxscore Type: float. Maximum score of feature to extract. If this is less than or equal to the maximum score, then any score is permitted.This is an optional parameter. 0.0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter tag Type: string. Tag of feature to extract. 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', or '/usedin'. By default any feature tag in the feature table is extracted. You can set this to match any feature tag you wish to show. The tag may be wildcarded by using '*'. If you wish to extract more than one tag, separate their names with the character '|', eg: gene | label. This is an optional parameter. * false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter value Type: string. Value of feature tags to extract. 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 a space or the character '|', eg: pax* | 10. This is an optional parameter. * false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter join Type: boolean. Some features, such as CDS (coding sequence) and mRNA are composed of exons concatenated together. There may be other forms of 'joined' sequence, depending on the feature table. If this option is set TRUE, then any group of these features will be output as a single sequence. If the 'before' and 'after' qualifiers have been set, then only the sequence before the first feature and after the last feature are added. False by default. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter featinname Type: boolean. To aid you in identifying the type of feature that has been output, the type of feature is added to the start of the description of the output sequence. Sometimes the description of a sequence is lost in subsequent processing of the sequences file, so it is useful for the type to be a part of the sequence ID name. If you set this to be TRUE then the name is added to the ID name of the output sequence. The default value is 'false'. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter describe Type: string. To aid you in identifying some further properties of a feature that has been output, this lets you specify one or more tag names that should be added to the output sequence description text, together with their values (if any). For example, if this is set to be 'gene', then if any output feature has the tag (for example) '/gene=BRCA1' associated with it, then the text '(gene=BRCA1)' will be added to the description line. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter osformat Type: string. Format of the output sequence (outseq). 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. The default value is 'fasta'. fasta false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter report Type: string. A general report for the underlying analysis job. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter detailed_status Type: long. The exit code of the underlying analysis job, 0 means the job returned normally. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter outseq Returns extracted features from a sequence. false http://www.mygrid.org.uk/ontology#biological_sequence String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter http://www.mygrid.org.uk/ontology#EMBL_nucleotide_sequence_database Soaplab service