GNV-1 WEB SERVICES

Bioinformatics and Genomics Node


OVERVIEW	WEBSERVICES	WORKFLOWS	CLIENTS	CONTACT US


	Web services

	All the services below are registered under the following authority, genome.imim.es. They can be discovered through the icapture BioMoby registry as well as through the one maintained by the INB. These services below do not support asynchronous protocol.
	Analysis GeneID v1.2: runGeneIDGFF: Reads a DNA Sequence and returns GeneID predictions in GFF format. service specifications input xml, execute it using MOWServ. translateGeneIDGFFPredictions: Reads a Nucleotide Sequence and Geneid predictions in GFF format and returns a collection of AminoAcid Sequences. service specifications DNA sequence input xml. SGP2: runSGP2GFF: Reads a DNA Sequence and tblastx report and returns GeneID predictions in GFF format. service specifications DNA sequence input xml. MatScan: runMatScanGFF: Reads a DNA Sequence and returns a map of putative Transcription Factor binding sites in GFF format. You can select either Transfac (v6.4) or Jaspar motifs collections. service specifications input xml. runMatScanGFFCollection: Reads a collection of Nucleotide Sequences and returns a collection of maps of putative binding sites in GFFF format. service specifications input xml. Meta-alignment: runMetaAlignment: Reads two binding sites maps in GFF format and returns the pairwise alignments of these maps in meta-alignment format. service specifications map1 xml and map2 xml. runMetaAlignmentGFF: Reads two binding sites maps in GFF format and returns the pairwise alignments of these maps in GFF format. service specifications map1 xml and map2 xml. runMultiPairwiseMetaAlignment: Reads a collection of binding sites maps in GFF format and returns a collection of pairwise alignments in meta-alignment format. It generates the map pairs internally, and runs meta-alignment for each pair of maps. service specifications input xml. runMultiPairwiseMetaAlignmentGFF: Reads a collection of binding sites maps in GFF format and returns a collection of pairwise alignments in GFF format. It generates the map pairs internally, and runs meta-alignment for each pair of maps. service specifications input xml. fromMetaAlignmentsToScoreMatrix: Reads a collection of pairwise meta-alignment outputs and returns a score matrix in xml format. service specifications input xml. fromMetaAlignmentsToTextScoreMatrix: Reads a collection of pairwise meta-alignment outputs and returns a score matrix in text format. service specifications input xml. Multiple Meta-alignment: runMultiMetaAlignment: Reads a set of binding sites maps in GFF format and returns the multiple alignment of these maps in meta-alignment format. service specifications input xml. runMultiMetaAlignmentGFF: Reads a set of binding sites maps in GFF format and returns the multiple alignment of these maps in GFF format. service specifications input xml. MEME v3.5.2: runMemeText: reads a collection of generic sequences (it can be either AminoAcid sequences or Nucleotide sequences) and returns predicted MEME motifs in MEME Text output. service specifications input xml. runMemeHTML: reads a collection of generic sequences (it can be either AminoAcid sequences or Nucleotide sequences) and returns predicted MEME motifs in MEME HTML output. service specifications input xml. parseMotifMatricesFromMEME: read MEME Text output and returns the set of predicted MEME motifs as a a collection of Matrix objects. service specifications input xml. RepeatMasker v3.1.5: runRepeatMasker: reads a DNA sequence and returns a masked DNA sequence. service specifications input xml. runRepeatMaskerCollection: reads a collection of DNA sequences and returns masked DNA sequences. service specifications input xml. Dust: runDust: reads a DNA sequence and returns low-complexity masked DNA sequence. service specifications input xml. runDustCollection: reads a collection of DNA sequences and returns low-complexity masked DNA sequences. service specifications input xml. runDustFASTA_NA_multi: reads a set of DNA sequences in FASTA format and returns low-complexity masked DNA sequences. service specifications input xml. SOTA: runSOTAClustering: runs SOTA algorithm to partition the gene space into subclusters and to also produce a gene tree. The input is a gene score matrix represented as a MicroArrayData_Text object. service specifications input xml. K-means: runKMeansClustering: runs K-means algorithm to partition the gene space into subclusters. The input is a gene score matrix represented as a MicroArrayData_Text object. service specifications input xml. Retrieval Ensembl: getUpstreamSeqFromEnsembl. Reads a List_Text object (representation of a list of Ensembl gene identifiers) and returns the upstream sequence of these given genes from Ensembl. service specifications input xml (a set of human genes). getOrthologousUpstreamSeqFromEnsembl. Reads an object (an Ensembl gene identifier) and returns the upstream sequence of all Ensembl predicted orthologues of this given gene. service specifications input xml (human leptin gene). Conversion fromGenericSequenceToFASTA. Reads a GenericSequence object and converts it into FASTA format. service specifications input xml. fromGenericSequenceCollectionToFASTA. Reads a collection of GenericSequence objects and converts it into FASTA format. service specifications input xml. fromFASTAToDNASequence. Reads a DNA sequence in FASTA format and returns a DNASequence object. service specifications input xml. fromFASTAToDNASequenceCollection. Reads a set of DNA sequences in FASTA format and returns a collection of DNASequence objects. service specifications input xml. fromFASTAToAminoAcidSequence. Reads an AminoAcid sequence in FASTA format and returns an AminoAcidSequence object. service specifications input xml. fromFASTAToAminoAcidSequenceCollection. Reads a set of AminoAcid sequences in FASTA format and returns a collection of AminoAcidSequence objects. service specifications input xml.