getorf European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_gene_finding.getorf http://www.ebi.ac.uk/soaplab/emboss4/services/nucleic_gene_finding.getorf?wsdl Finds and extracts open reading frames(ORFs). Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/getorf.html getorf Finds and extracts open reading frames(ORFs). Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/getorf.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 sequence_direct_data Type: string. DNA sequence. Choose this parameter if you want to provide the 'sequence' value as string (DNA sequence). 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. 1 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 table Type: string. Genetics code used for the translation. This is an optional parameter. The allowed values for this parameter are: 0 (Standard)| 1 (Standard (with alternative initiation codons))| 2 (Vertebrate Mitochondrial)| 3 (Yeast Mitochondrial)| 4 (Mold, Protozoan, Coelenterate Mitochondrial and Mycoplasma/Spiroplasma)| 5 (Invertebrate Mitochondrial)| 6 (Ciliate Macronuclear and Dasycladacean)| 9 (Echinoderm Mitochondrial)| 10 (Euplotid Nuclear)| 11 (Bacterial)| 12 (Alternative Yeast Nuclear)| 13 (Ascidian Mitochondrial)| 14 (Flatworm Mitochondrial)| 15 (Blepharisma Macronuclear)| 16 (Chlorophycean Mitochondrial)| 21 (Trematode Mitochondrial)| 22 (Scenedesmus obliquus)| 23 (Thraustochytrium Mitochondrial)| The default is 0. 0 false String minsize Type: long. Minimum nucleotide size of ORF to report. This is an optional parameter. The default is 30. 30 false String maxsize Type: long. Maximum nucleotide size of ORF to report. This is an optional parameter. The default is 1000000 1000000 false String find Type: string. This is a small menu of possible output options. The first four options are to select either the protein translation or the original nucleic acid sequence of the open reading frame. There are two possible definitions of an open reading frame: it can either be a region that is free of STOP codons or a region that begins with a START codon and ends with a STOP codon. The last three options are probably only of interest to people who wish to investigate the statistical properties of the regions around potential START or STOP codons. The last option assumes that ORF lengths are calculated between two STOP codons. This is an optional parameter. The allowed values for this parameter are: 0 (Translation of regions between STOP codons)| 1 (Translation of regions between START and STOP codons)| 2 (Nucleic sequences between STOP codons)| 3 (Nucleic sequences between START and STOP codons)| 4 (Nucleotides flanking START codons)| 5 (Nucleotides flanking initial STOP codons)| 6 (Nucleotides flanking ending STOP codons)| The default is 0. 0 false String methionine Type: boolean(Yes/No). START codons at the beginning of protein products will usually code for Methionine, despite what the codon will code for when it is internal to a protein. This qualifier sets all such START codons to code for Methionine by default. This is an optional parameter. The default is 'yes'. true false String circular Type: boolean(Yes/No). Is the sequence circular. This is an optional parameter. The default is 'No'. false false String reverse Type: boolean (Yes/No). Set this to be false if you do not wish to find ORFs in the reverse complement of the sequence. This is an optional parameter. The default is 'Yes'. true false String flanking Type: long. If you have chosen one of the options of the type of sequence to find that gives the flanking sequence around a STOP or START codon, this allows you to set the number of nucleotides either side of that codon to output. If the region of flanking nucleotides crosses the start or end of the sequence, no output is given for this codon. This is an optional parameter. The default is 100. 100 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 open reading frames of specified DNA sequence. false http://www.mygrid.org.uk/ontology#protein_sequence String http://www.mygrid.org.uk/ontology#searching http://www.mygrid.org.uk/ontology#EMBL_nucleotide_sequence_database Soaplab service