msbar European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_mutation.msbar http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_mutation.msbar?wsdl Changes a sequence a lot or a little, attempting to emulate various forms of mutation. You can set the number and types of mutations. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/msbar.html msbar Changes a sequence a lot or a little, attempting to emulate various forms of mutation. You can set the number and types of mutations. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/msbar.html sequence_usa Type: string. Any 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 http://www.mygrid.org.uk/ontology#EMBL_accession String sequence_direct_data Type: string. Any 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 sformat1 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. By default the service autodetects the sequence format. false String sbegin1 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. false String send1 Type: long. The last position to be used in the sequence. This is an optional parameter. By default it is the end the sequence. false String sprotein1 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. false String snucleotide1 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. false String sreverse1 Type: boolean. Use reverse complement of the nucleic acid sequence. This is an optional parameter. False by default. false String slower1 Type: boolean. Convert the sequence to lower case. This is an optional parameter. False by default. false String supper1 Type: boolean. Convert the sequence to UPPER case. This is an optional parameter. False by default. false String count Type: long. Number of times to perform the mutation operations. This is a mandatory parameter. The default is 1. 1 false String point_0 Type: boolean(true/false). No point mutation. This is an optional parameter. The default is 'true' true false String point_1 Type: boolean(true/false). Any point mutations(Insertions, Deletion, Changes, Duplication, Moves). This is an optional parameter. The default is 'false'. false false String point_2 Type: boolean(true/false). Point mutation to perform: INSERTIONS. This is an optional parameter. The default is 'false'. false false String point_3 Type: boolean(true/false). Point mutation to perform: DELETIONS. This is an optional parameter. The default is 'false'. false false String point_4 Type: boolean(true/false). Point mutation to perform: CHANGES. This is an optional parameter. The default is 'false'. false false String point_5 Type: boolean(true/false). Point mutation to perform: DUPLICATIONS. This is an optional parameter. The default is 'false'. false false String point_6 Type: boolean(true/false). Point mutation to perform: MOVES. This is an optional parameter. The default is 'false'. false false String block_0 Type: boolean(true/false). No bock mutation. This is an optional parameter. The default is 'true' true false String block_1 Type: boolean(true/false). Any block mutations(Insertions, Deletion, Changes, Duplication, Moves). This is an optional parameter. The default is 'false'. false false String block_2 Type: boolean(true/false). Block mutation to perform: INSERTIONS. This is an optional parameter. The default is 'false'. false false String block_3 Type: boolean(true/false). Block mutation to perform: DELETION . This is an optional parameter. The default is 'false'. false false String block_4 Type: boolean(true/false). Block mutation to perform: CHANGES. This is an optional parameter. The default is 'false'. false false String block_5 Type: boolean(true/false). Block mutation to perform: DUPLICATION. This is an optional parameter. The default is 'false'. false false String block_6 Type: boolean(true/false). Block mutation to perform: MOVES. This is an optional parameter. The default is 'false'. false false String othersequence_usa Type: string. If you require that the resulting mutated sequence should not match a set of other sequences, then you can specify that set of sequences here. For example, if you require that the mutated sequence should not be the same as the input sequence, enter the input sequence here. If you want the result to be different to previous results of this program, specify the previous result sequences here. The program will check that the result does not match the sequences specified here before writing it out. If a match is found, then the mutation is started again with a fresh copy of the input sequence. If, after 10 such retries, there is still a match to the set of sequence given here, then the matching mutated sequence is written with a warning message. 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 othersequence_direct_data parameter but not both together. Parameter mandatory if the othersequence_direct_data parameter has not been chosen. asis:N false http://www.mygrid.org.uk/ontology#EMBL_accession String othersequence_direct_data Type: string. If you require that the resulting mutated sequence should not match a set of other sequences, then you can specify that set of sequences here. For example, if you require that the mutated sequence should not be the same as the input sequence, enter the input sequence here. If you want the result to be different to previous results of this program, specify the previous result sequences here. The program will check that the result does not match the sequences specified here before writing it out. If a match is found, then the mutation is started again with a fresh copy of the input sequence. If, after 10 such retries, there is still a match to the set of sequence given here, then the matching mutated sequence is written with a warning message. Any valid sequence. Choose this parameter if you want to provide the 'sequence' value as string. Parameter mandatory if the othersequence_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 sformat2 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. By default the service autodetects the sequence format. false String sbegin2 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. false String send2 Type: long. The last position to be used in the sequence. This is an optional parameter. By default it is the end the sequence. false String sprotein2 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. false String snucleotide2 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. false String sreverse2 Type: boolean. Use reverse complement of the nucleic acid sequence. This is an optional parameter. False by default. false String slower2 Type: boolean. Convert the sequence to lower case. This is an optional parameter. False by default. false String supper2 Type: boolean. Convert the sequence to UPPER case. This is an optional parameter. False by default. false String codon_0 Type: boolean(true/false). No codon mutation. This is an optional parameter. The default is 'true' true false String codon_1 Type: boolean(true/false). Any codon mutations(Insertions, Deletion, Changes, Duplication, Moves). These are only done if the sequence is nucleic. This is an optional parameter. The default is 'false'. false false String codon_2 Type: boolean(true/false). Codon mutation to perform if the sequence is nucleic: INSERTIONS. This is an optional parameter. The default is 'false'. false false String codon_3 Type: boolean(true/false). Codon mutation to perform if the sequence is nucleic: DELETIONS. This is an optional parameter. The default is 'false'. false false String codon_4 Type: boolean(true/false). Codon mutation to perform if the sequence is nucleic: CHANGES. This is an optional parameter. The default is 'false'. false false String codon_5 Type: boolean(true/false). Codon mutation to perform if the sequence is nucleic: DUPLICATIONS. This is an optional parameter. The default is 'false'. false false String codon_6 Type: boolean(true/false). Codon mutation to perform if the sequence is nucleic: MOVES. This is an optional parameter. The default is 'false'. false false String inframe Type: boolean(true/false). Do 'codon' and 'block' operations in frame. This is an optional parameter. The default is 'false' false false String minimum Type: long. Minimum size for a block mutation. This is an optional parameter. The default is 1. 1 false String maximum Type: long. Maximum size for a block mutation. This is an optional parameter. The default is 10. 10 false String 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 is 'fasta'. fasta false 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 outseq Returns mutated sequence. false http://www.mygrid.org.uk/ontology#biological_sequence http://www.mygrid.org.uk/ontology#single_sequence_format String http://www.mygrid.org.uk/ontology#manipulating http://www.mygrid.org.uk/ontology#EMBL_nucleotide_sequence_database Soaplab service