esim4 European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_global.esim4 http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_global.esim4?wsdl Align a transcribed and spliced DNA sequence (mRNA) to a genomic DNA sequence. Detailed info about this operation can be found at the following link: http://www.embracegrid.info/dokuwiki/doku.php?id=tools:esim4 esim4 Align a transcribed and spliced DNA sequence (mRNA) to a genomic DNA sequence. Detailed info about this operation can be found at the following link: http://oryx.ulb.ac.be/embosshelp/sim4_lav.html asequence_usa Parameter type: string. 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 asequence_direct_data parameter but not both together. Parameter mandatory if the asequence_direct_data parameter hasn't been chosen. false String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter asequence_direct_data Type: string. DNA sequence. Choose this parameter if you want to provide the 'asequence' value as string. Parameter mandatory if the asequence_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 http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter 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. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter sbegin1 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 http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter send1 Type: long. The last position to be used in the sequence. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter sprotein1 Type: boolean. Is the sequence a protein? This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter snucleotide1 Type: boolean. Is the sequence a nucleotide? This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter sreverse1 Type: boolean. Use reverse complement of the nucleic acid sequence. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter slower1 Type: boolean. Convert the sequence to lower case. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter supper1 Type: boolean. Convert the sequence to UPPER case. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter bsequence_usa Parameter type: string. 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 asequence_direct_data parameter but not both together. Parameter mandatory if the asequence_direct_data parameter hasn't been chosen. false String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter bsequence_direct_data Type: string. genomic sequence. Choose this parameter if you want to provide the 'bsequence' value as string. Parameter mandatory if the bsequence_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 http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter 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. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter sbegin2 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 http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter send2 Type: long. The last position to be used in the sequence. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter sprotein2 Type: boolean. Is the sequence a protein? This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter snucleotide2 Type: boolean. Is the sequence a nucleotide? This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter sreverse2 Type: boolean. Use reverse complement of the nucleic acid sequence. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter slower2 Type: boolean. Convert the sequence to lower case. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter supper2 Type: boolean. Convert the sequence to UPPER case. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter word Type: long. Sets the word size for blast hits. Default value: 12. This is an optional parameter. 12 String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter extend Type: long. Sets the word extension termination limit for the blast-like stage of the algorithm. Default value:12. This is an optional parameter. 12 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter cutoff Type: long. Sets the cutoff (E) in range [3,10]. This is an optional parameter. 3 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter usermspa Type: boolean. if False: esim4 program calculates mspA, if True: value required for mspA. This is an optional parameter. N false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter mspa Type: long. MSP (Maximal Segment Pair) score threshold for the first stage of the algorithm. (If this option is not specified, the threshold is computed from the lengths of the sequences, using statistical criteria.) For example, a good value for genomic sequences in the range of a few hundred Kb is 16. To avoid spurious matches, a larger value may be needed for longer sequences.This is an optional parameter. 16 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter usermspb Type: boolean. if false: esim4 program calculates mspB, if True: value required for mspB . This is an optional parameter. N false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter mspb Type: long. Sets the threshold for the MSP(Maximal Segment Pair) scores when aligning the as-yet-unmatched fragments, during the second stage of the algorithm. By default, the constant 12 and a statistics-based threshold is chosen. This is an optional parameter. 12 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter weight Type: long. Weight value. Default value: 0. Any value given must be positive. This is an optional parameter. 0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter diagonal Type: long. Bound for the diagonal distance within consecutive MSPs (Maximal Segment Pair)in an exon. For example 10. This is an optional parameter. 10 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter strand_both Type: boolean. This determines the strand of the genome with which the mRNA will be aligned. The default value is 'both', in which case both strands of the genome are attempted. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter strand_forward Type: boolean. Forward strand only. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter strand_reverse Type: boolean. Reverse strand only. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter format Type: long. Sets the output format. This is an optional parameter. 0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter cliptails Type: boolean. Trim poly-A tails. Specifies whether or not the program should report the fragment of the alignment containing the poly-A tail (if found). This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter smallexons Type: boolean. Requests an additional search for small marginal exons guided by the splice-site recognition signals. This option can be used when a high accuracy match is expected. The default value is false, specifying no additional search. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter ambiguity Type: boolean. Controls the set of characters allowed in the input sequences. By default, ambiguity characters (ABCDGHKMNRSTVWXY) are allowed. By specifying "false", the set of acceptable characters is restricted to A,C,G,T,N and X only. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter cdsregion Type: string. Allows the user to specify the endpoints of the CDS in the input mRNA. This option is only available with the "format=5" flag, which produces output in the format required by PipMaker. Alternatively, the CDS coordinates could appear in a construct CDS=n1..n2 in the FastA header of the mRNA sequence. EMBOSS known type: Sequence range in the format nn..nn. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter offseta Type: long. Some sort of offset in first sequence. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter offsetb Type: long. Some sort of offset in second sequence. This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter toa Type: long. Offset end of first sequence? This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter tob Type: long. Offset end of second sequence? This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter 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 Returns a sequence alignment report false http://www.mygrid.org.uk/ontology#pairwise_sequence_alignment_report String http://www.mygrid.org.uk/ontology#pairwise_local_aligning Soaplab service