matrix_scan

Contributor URLhttp://rsat.bigre.ulb.ac.be/rsat/web_services/RSATWS_documentation.xml

WSDL URLhttp://rsat.bigre.ulb.ac.be/rsat/web_services/RSATWS.wsdl PASSED

Part of the Regulatory Sequence Analysis Tools (RSAT).

Scans sequences with one or several position-specific scoring matrices (PSSM) to identify instances of the corresponding motifs (putative sites). This program supports a variety of background models (Bernoulli, Markov chains of any order).

A description of the WSDL service:

RSATWebServices

Namespace: urn:RSATWS

Web services for the Regulatory Sequence Analysis Tools (RSAT). Tools developed by Jacques van Helden (jvanheld@bigre.ulb.ac.be), SOAP/WSDL interface developed by Olivier Sand (oly@bigre.ulb.ac.be).

Port: RSATWSPortType
Location: http://rsat.ulb.ac.be/rsat/web_services/RSATWS.cgi
Protocol: http://schemas.xmlsoap.org/soap/http
Default Style: document

Operations

retrieve_seq

Returns upstream, downstream or coding DNA sequences for list of query genes.

SOAP Action:
Input Message: retrieve_seqRequest
- parameters
  - retrieve_seq type
    - request type RetrieveSequenceRequest
      - output type string
      - organism type string
      - query type string
      - all type int
      - noorf type int
      - from type int
      - to type int
      - feattype type string
      - type type string
      - format type string
      - lw type int
      - label type string
      - label_sep type string
      - nocom type int
      - repeat type int
      - imp_pos type int
Output Message: retrieve_seqResponse
- output
  - retrieve_seqResponse type
    - response type RetrieveSequenceResponse
      - server type string
      - command type string
      - client type string

retrieve_seq_multigenome

Returns upstream, downstream or coding DNA sequencesfor list of query genes and organisms.

SOAP Action:
Input Message: retrieve_seq_multigenomeRequest
- parameters
  - retrieve_seq_multigenome type
    - request type RetrieveSequenceMultigenomeRequest
      - output type string
      - input type string
      - tmp_input_file type string
      - all type int
      - noorf type int
      - from type int
      - to type int
      - feattype type string
      - type type string
      - format type string
      - lw type int
      - label type string
      - label_sep type string
      - nocom type int
      - repeat type int
      - imp_pos type int
      - gene_col type int
      - org_col type int
Output Message: retrieve_seq_multigenomeResponse
- output
  - retrieve_seq_multigenomeResponse type
    - response type RetrieveSequenceMultigenomeResponse
      - server type string
      - command type string
      - client type string

retrieve_ensembl_seq

Returns upstream, downstream or coding DNA sequences for list of query genes (in EnsEMBL database).

SOAP Action:
Input Message: retrieve_ensembl_seqRequest
- parameters
  - retrieve_ensembl_seq type
    - request type RetrieveEnsemblSequenceRequest
      - output type string
      - organism type string
      - ensembl_host type string
      - db_name type string
      - query type string
      - tmp_infile type string
      - all type int
      - noorf type int
      - nogene type int
      - from type int
      - to type int
      - feattype type string
      - type type string
      - chromosome type string
      - left type int
      - right type int
      - strand type int
      - features type string
      - feat_format type string
      - mask_coding type int
      - repeat type int
      - all_transcripts type int
      - unique_sequences type int
      - first_intron type int
      - non_coding type int
      - utr type string
      - line_width type int
      - ortho type int
      - taxon type string
      - homology_type type string
      - header_organism type string
Output Message: retrieve_ensembl_seqResponse
- output
  - retrieve_ensembl_seqResponse type
    - response type RetrieveEnsemblSequenceResponse
      - server type string
      - command type string
      - client type string

purge_seq

Mask repeated fragments of an input sequence.

SOAP Action:
Input Message: purge_seqRequest
- parameters
  - purge_seq type
    - request type PurgeSequenceRequest
      - output type string
      - sequence type string
      - tmp_infile type string
      - format type string
      - match_length type int
      - mismatch type int
      - str type int
      - delete type int
      - mask_short type int
Output Message: purge_seqResponse
- output
  - purge_seqResponse type
    - response type PurgeSequenceResponse
      - server type string
      - command type string
      - client type string

oligo_analysis

Analysis of the statistical significance of all the oligomers of a given size in a sequence. Commonly used to detect over-represented oligonucleotides in a set of promoter sequences.

SOAP Action:
Input Message: oligo_analysisRequest
- parameters
  - oligo_analysis type
    - request type OligoAnalysisRequest
      - output type string
      - verbosity type int
      - sequence type string
      - tmp_infile type string
      - format type string
      - length type int
      - organism type string
      - background type string
      - stats type string
      - noov type int
      - str type int
      - sort type int
      - lth type string
      - uth type string
      - pseudo type string
Output Message: oligo_analysisResponse
- output
  - oligo_analysisResponse type
    - response type OligoAnalysisResponse
      - server type string
      - command type string
      - client type string

dyad_analysis

Analysis of the statistical significance of all the spaced dyads of a given size in a sequence. Commonly used to detect over-represented spaced dyads in a set of promoter sequences.

SOAP Action:
Input Message: dyad_analysisRequest
- parameters
  - dyad_analysis type
    - request type DyadAnalysisRequest
      - output type string
      - verbosity type int
      - sequence type string
      - tmp_infile type string
      - format type string
      - length type int
      - spacing type string
      - organism type string
      - background type string
      - stats type string
      - type type string
      - noov type int
      - str type int
      - sort type int
      - under type int
      - two_tails type int
      - zeroocc type int
      - lth type string
      - uth type string
Output Message: dyad_analysisResponse
- output
  - dyad_analysisResponse type
    - response type DyadAnalysisResponse
      - server type string
      - command type string
      - client type string

pattern_assembly

Assemble a set of oligonucleotides or dyads into groups of overlapping patterns (assemblies).

SOAP Action:
Input Message: pattern_assemblyRequest
- parameters
  - pattern_assembly type
    - request type PatternAssemblyRequest
      - output type string
      - input type string
      - tmp_infile type string
      - verbosity type int
      - score_col type int
      - str type int
      - maxfl type int
      - subst type int
      - max_asmb_nb type int
      - max_asmb_size type int
      - maxpat type int
      - toppat type int
Output Message: pattern_assemblyResponse
- output
  - pattern_assemblyResponse type
    - response type PatternAssemblyResponse
      - server type string
      - command type string
      - client type string

dna_pattern

Searches all occurrences of a pattern within DNA sequences.

SOAP Action:
Input Message: dna_patternRequest
- parameters
  - dna_pattern type
    - request type DnaPatternRequest
      - output type string
      - sequence type string
      - tmp_infile type string
      - format type string
      - subst type int
      - pattern type string
      - pattern_file type string
      - tmp_pattern_file type string
      - id type string
      - origin type string
      - noov type int
      - score type int
      - str type int
      - sort type int
      - th type int
      - return type string
Output Message: dna_patternResponse
- output
  - dna_patternResponse type
    - response type DnaPatternResponse
      - server type string
      - command type string
      - client type string

convert_features

Interconversions between various formats of feature description.

SOAP Action:
Input Message: convert_featuresRequest
- parameters
  - convert_features type
    - request type ConvertFeaturesRequest
      - output type string
      - input type string
      - tmp_infile type string
      - from type string
      - to type string
Output Message: convert_featuresResponse
- output
  - convert_featuresResponse type
    - response type ConvertFeaturesResponse
      - server type string
      - command type string
      - client type string

feature_map

Draws a graphical map of features (e.g. results of pattern matching) in a set of sequences.

SOAP Action:
Input Message: feature_mapRequest
- parameters
  - feature_map type
    - request type FeatureMapRequest
      - output type string
      - features type string
      - tmp_infile type string
      - sequence type string
      - tmp_sequence_file type string
      - sequence_format type string
      - format type string
      - from type int
      - to type int
      - title type string
      - label type string
      - symbol type int
      - dot type int
      - mlen type int
      - mapthick type int
      - mspacing type int
      - origin type int
      - legend type int
      - scalebar type int
      - scalestep type int
      - scorethick type int
      - maxscore type int
      - minscore type int
      - maxfthick type int
      - minfthick type int
      - htmap type int
      - mono type int
      - orientation type string
      - select type string
Output Message: feature_mapResponse
- output
  - feature_mapResponse type
    - response type FeatureMapResponse
      - server type string
      - command type string
      - client type string

footprint_discovery

Detect phylogenetic footprints by applying dyad-analysis in promoters of a set of orthologous genes.

SOAP Action:
Input Message: footprint_discoveryRequest
- parameters
  - footprint_discovery type
    - request type FootprintDiscoveryRequest
      - output type string
      - verbosity type int
      - genes type string
      - tmp_infile type string
      - all_genes type int
      - max_genes type int
      - output_prefix type string
      - query type string
      - sep_genes type int
      - organism type string
      - taxon type string
      - index type int
      - lth type string
      - uth type string
      - return type string
      - to_matrix type int
      - bg_model type string
      - no_filter type int
      - infer_operons type int
      - dist_thr type int
Output Message: footprint_discoveryResponse
- output
  - footprint_discoveryResponse type
    - response type FootprintDiscoveryResponse
      - server type string
      - command type string
      - client type string

get_orthologs

Get orthologuous genes.

SOAP Action:
Input Message: get_orthologsRequest
- parameters
  - get_orthologs type
    - request type GetOrthologsRequest
      - output type string
      - organism type string
      - taxon type string
      - query type string
      - all type int
      - nogrep type int
      - return type string
      - lth type string
      - uth type string
Output Message: get_orthologsResponse
- output
  - get_orthologsResponse type
    - response type GetOrthologsResponse
      - server type string
      - command type string
      - client type string

infer_operon

Infer operon.

SOAP Action:
Input Message: infer_operonRequest
- parameters
  - infer_operon type
    - request type InferOperonRequest
      - output type string
      - organism type string
      - query type string
      - tmp_infile type string
      - all type int
      - distance type int
      - return type string
Output Message: infer_operonResponse
- output
  - infer_operonResponse type
    - response type InferOperonResponse
      - server type string
      - command type string
      - client type string

gene_info

Get information about genes.

SOAP Action:
Input Message: gene_infoRequest
- parameters
  - gene_info type
    - request type GeneInfoRequest
      - output type string
      - organism type string
      - query type string
      - full type int
      - noquery type int
      - descr type int
      - feattype type string
Output Message: gene_infoResponse
- output
  - gene_infoResponse type
    - response type GeneInfoResponse
      - server type string
      - command type string
      - client type string

supported_organisms

List RSAT suppported organisms.

SOAP Action:
Input Message: supported_organismsRequest
- parameters
  - supported_organisms type
    - request type SupportedOrganismsRequest
      - output type string
      - format type string
      - taxon type string
Output Message: supported_organismsResponse
- output
  - supported_organismsResponse type
    - response type SupportedOrganismsResponse
      - server type string
      - command type string
      - client type string

text_to_html

Converts a tab-delimited file into a HTML table

SOAP Action:
Input Message: text_to_htmlRequest
- parameters
  - text_to_html type
    - request type TextToHtmlRequest
      - output type string
      - inputfile type string
      - chunk type int
      - no_sort type int
      - font type string
Output Message: text_to_htmlResponse
- output
  - text_to_htmlResponse type
    - response type TextToHtmlResponse
      - server type string
      - command type string
      - client type string

parse_psi_xml

Converts a psi xml file in a tab delimited file

SOAP Action:
Input Message: parse_psi_xmlRequest
- parameters
  - parse_psi_xml type
    - request type parsepsixmlRequest
      - output type string
      - inputfile type string
      - channels type string
      - interactor_type type string
      - uth type float
      - lth type float
Output Message: parse_psi_xmlResponse
- output
  - parse_psi_xmlResponse type
    - response type parsepsixmlResponse
      - server type string
      - command type string
      - client type string

roc_stats

Computes, from a set of scored results associated with validation labels, the derived statistics (Sn, PPV, FPR), which can be further used to draw a ROC curve.

SOAP Action:
Input Message: roc_statsRequest
- parameters
  - roc_stats type
    - request type RocStatsRequest
      - output type string
      - inputfile type string
      - scol type int
      - lcol type int
      - status type string
      - total type int
Output Message: roc_statsResponse
- output
  - roc_statsResponse type
    - response type RocStatsResponse
      - server type string
      - command type string
      - client type string

classfreq

This script takes a group of numbers (real or integers) and outputs their distribution among classes.

SOAP Action:
Input Message: classfreqRequest
- parameters
  - classfreq type
    - request type ClassFreqRequest
      - output type string
      - inputFile type string
      - classinterval type string
      - col type string
      - min type string
      - max type string
      - from type string
      - to type string
Output Message: classfreqResponse
- output
  - classfreqResponse type
    - response type ClassFreqResponse
      - server type string
      - command type string
      - client type string

xygraph

Plot a graph and export it.

SOAP Action:
Input Message: xygraphRequest
- parameters
  - xygraph type
    - request type XYGraphRequest
      - output type string
      - inputFile type string
      - format type string
      - title1 type string
      - title2 type string
      - lines type int
      - legend type int
      - header type int
      - xleg1 type string
      - xleg2 type string
      - yleg1 type string
      - yleg2 type string
      - xmax type string
      - ymax type string
      - xmin type string
      - ymin type string
      - ylog type string
      - xlog type string
      - xcol type string
      - ycol type string
Output Message: xygraphResponse
- output
  - xygraphResponse type
    - response type XYGraphResponse
      - server type string
      - command type string
      - client type string

convert_seq

Converts a sequence between two formats (e.g. fasta -> raw).

SOAP Action:
Input Message: convert_seqRequest
- parameters
  - convert_seq type
    - request type ConvertSeqRequest
      - output type string
      - sequence type string
      - tmp_infile type string
      - from type string
      - to type string
Output Message: convert_seqResponse
- output
  - convert_seqResponse type
    - response type ConvertSeqResponse
      - server type string
      - command type string
      - client type string

compare_classes

Compare two class files(the query file and the reference file). Each class of the query file is compared to each class of the reference file. The number of common elements is reported, as well as the probability to observe at least this number of common elements by chance alone.

SOAP Action:
Input Message: compare_classesRequest
- parameters
  - compare_classes type
    - request type CompareClassesRequest
      - output type string
      - ref_classes type string
      - query_classes type string
      - return_fields type string
      - score_column type int
      - input_classes type string
      - upper_threshold_field type string
      - upper_threshold_value type string
      - lower_threshold_field type string
      - lower_threshold_value type string
      - sort type string
      - distinct type int
      - triangle type int
      - matrix type string
Output Message: compare_classesResponse
- output
  - compare_classesResponse type
    - response type CompareClassesResponse
      - server type string
      - command type string
      - client type string

convert_classes

Interconversions between different formats of cluster files.

SOAP Action:
Input Message: convert_classesRequest
- parameters
  - convert_classes type
    - request type ConvertClassesRequest
      - output type string
      - informat type string
      - outformat type string
      - member_col type string
      - class_col type string
      - score_col type int
      - min_score type string
      - inputclasses type string
      - names type string
Output Message: convert_classesResponse
- output
  - convert_classesResponse type
    - response type ConvertClassesResponse
      - server type string
      - command type string
      - client type string

contingency_stats

This programs takes as input a contingency table, and calculates various matching statistics between the rows and columns. The description of these statistics can be found in Brohee and van Helden (2006).

SOAP Action:
Input Message: contingency_statsRequest
- parameters
  - contingency_stats type
    - request type ContingencyStatsRequest
      - output type string
      - inputfile type string
      - decimals type int
      - return type string
      - rsizes type string
      - csizes type string
Output Message: contingency_statsResponse
- output
  - contingency_statsResponse type
    - response type ContingencyStatsResponse
      - server type string
      - command type string
      - client type string

contingency_table

Create a contingency table from a two-column file.

SOAP Action:
Input Message: contingency_tableRequest
- parameters
  - contingency_table type
    - request type ContingencyTableRequest
      - output type string
      - inputfile type string
      - col1 type int
      - col2 type int
      - margin type int
      - null type int
Output Message: contingency_tableResponse
- output
  - contingency_tableResponse type
    - response type ContingencyTableResponse
      - server type string
      - command type string
      - client type string

matrix_scan

Scan sequences with one or several position-specific scoring matrices (PSSM) to identify instances of the corresponding motifs(putative sites). This program supports a variety of background models (Bernoulli, Markov chains of any order).

SOAP Action:
Input Message: matrix_scanRequest
- parameters
  - matrix_scan type
    - request type MatrixScanRequest
      - output type string
      - sequence type string
      - tmp_sequence_infile type string
      - matrix type string
      - tmp_matrix_infile type string
      - sequence_format type string
      - matrix_format type string
      - n_treatment type string
      - consensus_name type string
      - pseudo type int
      - equi_pseudo type int
      - top_matrices type int
      - background_model type string
      - tmp_background_infile type string
      - organism type string
      - background type string
      - background_input type int
      - background_window type int
      - markov type int
      - background_pseudo type float
      - return_fields type string
      - sort_distrib type int
      - lth type string
      - uth type string
      - str type int
      - verbosity type int
      - origin type string
      - decimals type int
      - crer_ids type int
Output Message: matrix_scanResponse
- output
  - matrix_scanResponse type
    - response type MatrixScanResponse
      - server type string
      - command type string
      - client type string

convert_matrix

Performs inter-conversions between various formats of position-specific scoring matrices (PSSM). The program also performs a statistical analysis of the original matrix to provide different position-specific scores (weight, frequencies, information contents), general statistics (E-value, total information content), and synthetic descriptions (consensus).

SOAP Action:
Input Message: convert_matrixRequest
- parameters
  - convert_matrix type
    - request type ConvertMatrixRequest
      - output type string
      - matrix type string
      - background_format type string
      - background_pseudo type float
      - from type string
      - to type string
      - return type string
      - sort type string
      - top type int
      - pseudo type float
      - equi_pseudo <

WSDL Changes

Date	Description of Changes
8th April 2009	First Snapshot
25th April 2009	Operation named random_graph - Input message part type has changed

Test #1: matrix_scan perl test 1

This test scans the upstream sequence of the Mus musculus HoxB1 sequence with two matrices and compares the matched sites to one of the expected ones.

Submitted by olisand on Tue, 09/02/2008 - 15:34