sirna European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_composition.sirna http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_composition.sirna?wsdl Finds siRNA duplexes in mRNA. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sirna.html sirna Finds siRNA duplexes in mRNA. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/5.0/emboss/apps/sirna.html sequence_usa Type: string. DNA or RNA seqquence. 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. DNA or RNA sequence. Choose this parameter if you want to provide the 'sequence' value (DNA sequence) as string. Parameter mandatory if the sequence_usa parameter hasn't been chosen. false http://www.mygrid.org.uk/ontology#DNA_sequence http://www.mygrid.org.uk/ontology#single_sequence_format 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. By default the service autodetects the sequence format. false 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. false String send 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 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. false 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. false String sreverse Type: boolean. Use reverse complement of the nucleic acid sequence. This is an optional parameter. False by default. false String slower Type: boolean. Convert the sequence to lower case. This is an optional parameter. False by default. false String supper Type: boolean. Convert the sequence to UPPER case. This is an optional parameter. False by default. false String poliii Type: boolean(Yes/No). This option allows you to select only the 21 base probes that start with a purine and so can be expressed from Pol III expression vectors. This is the NARN(17)YNN pattern that has been suggested by Tuschl et al. This is an optional parameter. The default is 'No'. false false String aa Type: boolean(Yes/No). This option allows you to select only those 23 base regions that start with 'AA'. If this option is not selected then regions that start with AA will be favoured by giving them a higher score, but regions that do not start with AA will also be reported. This is an optional parameter. The default is 'No'. false false String tt Type: boolean(Yes/No). This option allows you to select only those 23 base regions that end with TT. If this option is not selected then regions that end with TT will be favoured by giving them a higher score, but regions that do not end with TT will also be reported. This is an optional parameter. The default is 'No'. false false String polybase Type: boolean(Yes/No). If this option is FALSE then only those 23 base regions that have no repeat of 4 or more of any bases in a row will be reported. No regions will ever be reported that have 4 or more G's in a row. This is an optional parameter. The default is 'Yes'. true false String context Type: boolean(Yes/No). The output report gives the sequences of the 21 base siRNA regions ready to be ordered. This does not give you an indication of the 2 bases before the 21 bases. It is often interesting to see which of the suggested possible probe regions have an 'AA' in front of them (i.e. it is useful to see which of the 23 base regions start with an 'AA'). This option displays the whole 23 bases of the region with the first two bases in brackets, e.g. '(AA)' to give you some context for the probe region. YOU SHOULD NOT INCLUDE THE TWO BASES IN BRACKETS WHEN YOU PLACE AN ORDER FOR THE PROBES. The default is 'No'. false false String osformat Type: string. Output format of the sequences of the 23 base regions that the siRNAs are selected from. You may use it to do searches of mRNA databases (e.g. REFSEQ) to confirm that the probes are unique to the gene you wish to use it on. 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. false String detailed_status Type: long. The exit code of the underlying analysis job, 0 means the job returned normally. false String outfile The output is a table of the forward and reverse parts of the 21 base siRNA duplex. Both the forward and reverse sequences are written 5' to 3', ready to be ordered. The last two bases have been replaced by 'dTdT'. The starting position of the 23 base region and the %GC content is also given. If you wish to see the complete 23 base sequence, then either look at the sequence in the other output, or use the 'context' parameter which will display the 23 bases of the forward sequence in this report with the first two bases in brackets. These first two bases do not form part of the siRNA probe to be ordered. false String outseq Returns sequences of the 23 base regions that the siRNAs are selected from. You may use it to do searches of mRNA databases (e.g. REFSEQ) to confirm that the probes are unique to the gene you wish to use it on. false String http://www.mygrid.org.uk/ontology#predicting http://www.mygrid.org.uk/ontology#EMBL_nucleotide_sequence_database Soaplab service