trimest European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/edit.trimest http://www.ebi.ac.uk/soaplab/emboss4/services/edit.trimest?wsdl Trim poly-A tails off EST sequences. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/trimest.html trimest Trim poly-A tails off EST sequences. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/trimest.html sequence_usa Type: string. DNA 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 http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter sequence_direct_data Type: string. DNA 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#nucleotide_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 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 minlength Type: long. This is the minimum length that a poly-A (or poly-T) tail must have before it is removed. This is an optional parameter. The default value is 4. 4 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter mismatches Type: long. If there are this number or fewer contiguous non-A bases in a poly-A tail then, if there are 'minlength' 'A' bases before them, they will be considered part of the tail and removed . For example the terminal 4 A's of GCAGAAAA would be removed with the default values of 4 for 'minlength' parameter and 1 for mismatches parameters. (There are not at least 4 A's before the last 'G' and so only the A's after it are considered to be part of the tail). The terminal 9 bases of GCAAAAGAAAA would be removed; There are at least 'minlength' A's preceeding the last 'G', so it is part of the tail. This is an optional parameter. The default value is 1. 1 false String reverse Type: boolean. When a poly-T region at the 5' end of the sequence is found and removed, it is likely that the sequence is in the reverse sense. This option will change the sequence to the forward sense when it is written out. If this option is not set, then the sense will not be changed. This is an optional parameter. True by default. true false String tolower Type: string. The poly-A region can be 'masked' by converting the sequence characters to lower-case. Some non-EMBOSS programs e.g. fasta can interpret this as a masked region. The sequence is unchanged apart from the case change. You might like to ensure that the whole sequence is in upper-case before masking the specified regions to lower-case by using the 'supper' parameter. This is an optional parameter. The default value is 'No'. N false String fiveprime Type: boolean. If this is set true, then the 5' end of the sequence is inspected for poly-T tails. These will be removed if they are longer than any 3' poly-A tails. If this is false, then the 5' end is ignored. This is an optional parameter. The default value is 'true'. true 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 value 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 outseq Returns sequence without poly-A tails. false http://www.mygrid.org.uk/ontology#nucleotide_sequence http://www.mygrid.org.uk/ontology#single_sequence_format String http://www.mygrid.org.uk/ontology#removing http://www.mygrid.org.uk/ontology#EMBL_nucleotide_sequence_database Soaplab service