est2genome European Bioinformatics Institute http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_global.est2genome http://www.ebi.ac.uk/soaplab/emboss4/services/alignment_global.est2genome?wsdl Align EST and genomic DNA sequences. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/est2genome.html est2genome Align EST and genomic DNA sequences. Detailed info about this operation can be found at the following link: http://emboss.sourceforge.net/apps/release/4.0/emboss/apps/est2genome.html estsequence_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#secondaryParameter estsequence_direct_data Type: string. DNA sequence. Choose this parameter if you want to provide the 'estsequence' value as string. Parameter mandatory if the estsequence_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#secondaryParameter 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. String 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 genomesequence_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. true String http://www.mygrid.org.uk/mygrid-moby-service#simpleParameter genomesequence_direct_data Type: string. DNA sequence. Choose this parameter if you want to provide the 'genomesequence' value as string. Parameter mandatory if the genomesequence_usa parameter hasn't been chosen. EMBOSS known type: Unspliced genomic. false http://www.mygrid.org.uk/ontology#genome_nucleotide_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 match Type: long. Score for matching two bases. This is an optional parameter. 1 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter mismatch Type: long. Cost for mismatching two bases. This is an optional parameter. 1 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter gappenalty Type: long. Cost for deleting a single base in either sequence, excluding introns. This is an optional parameter. 2 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter intronpenalty Type: long. Cost for an intron, independent of length. This is an optional parameter. 40 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter splicepenalty Type: long. Cost for an intron, independent of length and starting/ending on donor-acceptor sites. This is an optional parameter. 20 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter minscore Type: long. Exclude alignments with scores below this threshold score. This is an optional parameter. 30 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter reverse Type: boolean. Reverse the orientation of the EST sequence. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter splice Type: boolean. Use donor and acceptor splice sites. If you want to ignore donor-acceptor sites then set this to be false. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter mode_both Type: boolean. This determines the comparion mode. The default value is 'both', in which case both strands of the EST are compared assuming a forward gene direction, and the best comparsion redone assuming a reversed gene splicing direction. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter mode_forward Type: boolean. Compare forward strand only. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter mode_reverse Type: boolean. Compare reverse strand only. This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter best Type: boolean. You can print out all comparisons instead of just the best one by setting this to be false. This is an optional parameter. true false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter space Type: float. For linear-space recursion. If product of sequence lengths divided by 4 exceeds this, then a divide-and-conquer strategy is used to control the memory requirements. In this way very long sequences can be aligned. If you have a machine with plenty of memory you can raise this parameter (but do not exceed the machine's physical RAM). This is an optional parameter. 10.0 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter shuffle Type: long. Shuffle (Any integer value). This is an optional parameter. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter seed Type: long. Random number seed. For example: 20825. This is an optional parameter. 20825 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter align Type: boolean. Show the alignment. The alignment includes the first and last 5 bases of each intron, together with the intron width. The direction of splicing is indicated by angle brackets (forward or reverse). This is an optional parameter. false false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter width Type: long. Alignment width. This is an optional parameter. 50 false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter report Type: string. A general report for the underlying analysis job. false String http://www.mygrid.org.uk/mygrid-moby-service#secondaryParameter 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