checktrans European Bioinformatics Institute http://www.ebi.ac.uk/ EBI http://www.ebi.ac.uk/soaplab/emboss4/services/protein_composition.checktrans http://www.ebi.ac.uk/soaplab/emboss4/services/protein_composition.checktrans?wsdl Reports STOP codons and ORF statistics of a protein. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/checktrans.html checktrans Reports STOP codons and ORF statistics of a protein. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/checktrans.html sequence_usa Type: string. Protein sequence with a possible stop. 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. String sequence_direct_data Type: string. Protein sequence with a possible stop. Choose this parameter if you want to provide the 'sequence' value as string (protein sequence). Parameter mandatory if the sequence_usa parameter hasn't been chosen. http://www.mygrid.org.uk/ontology#protein_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. 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. String send Type: long. The last position to be used in the sequence. This is an optional parameter. By default it is the end of the sequence. 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. 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. String sreverse Type: boolean. Use reverse complement of the nucleic acid sequence. This is an optional parameter. False by default. String slower Type: boolean. Convert the sequence to lower case. This is an optional parameter. False by default. String supper Type: boolean. Convert the sequence to UPPER case. This is an optional parameter. False by default. String orfml Type: long. Minimum ORF Length to report. This is an optional parameter. The default is 100. 100 String addlast Type: boolean(true/false). An asterisk in the protein sequence indicates the position of a STOP codon. Checktrans assumes that all ORFs end in a STOP codon. Forcing the sequence to end with an asterisk, if there is not one there already, makes checktrans treat the end as a potential ORF. If an asterisk is added, it is not included in the reported count of STOPs. This is an optional parameter. The default is 'true'. true String osformat Type: string. Output format. 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 String offormat Type: string. Format for output features. This is an optional parameter. The allowed values for this parameter are: embl, genbank, ddbj, gff, acedb, swissprot. The default is 'gff'. gff 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 outfile Returns the numeric count of the ORF, the position of the terminating STOP codon, the length of the ORF, its start and end positions and the name of the sequence it has been written out as. The name of the output sequences is constructed from the name of the input sequence followed by an underscore and then the numeric count of the ORF. String outfeat Returns features of the protein sequence String outseq Returns the protein sequence containing the predicted ORF. http://www.mygrid.org.uk/ontology#protein_sequence http://www.mygrid.org.uk/ontology#fasta_format String http://www.mygrid.org.uk/ontology#searching http://www.mygrid.org.uk/ontology#protein_sequence_database Soaplab service