RNAmmer

By | September 22, 2011

This Web Service predicts location of ribosomal RNA genes in full genome sequences
by using Hidden Markov Models based on alignments from a highly cureated dataset of
structurally aligned sequnces.

The input is one or more genomic sequence(s) as either one or more contigs. Each contig
is submitted as one continous string of DNA together with the sequences identifier.

The kingdom (either Bacteria, Archaea, or Eukaryotes) is specified once for each job
that is submitted, using the abbriviations ‘bac’, ‘arc’, and ‘euk’.

More information about the method can be found at:

http://www.cbs.dtu.dk/services/RNAmmer/

This service is fully asynchronous; the usage is split into the following
three operations, which is usually executed in this order.

Procedures and messages used are either common and shared among all the CBS
Web Services, or distinct to each individual Web Service. Marked [distinct] and
[common] respectively.

1. runService [distinct/common]
Submit the input parapeter(s) and sequence data and returns a job identifier

Input: [distinct]
* ‘mol’ -Molecule (e.g. ssu,lsu,tsu)
* ‘kingdom’ – The kingdom of the genomic sequence
3 kingdoms are available: bac, euk, arc. This is specified
only once for the sequences in the current job.
* ‘sequences’ – An array of sequence objects, containing the following elements:
* ‘ident’ – The identifier of the sequence
* ‘seq’ – The sequence specified as one continous string
Output: [common]
* ‘jobid’ – The 32 byte identification string of the job
* ‘datetime’ – The last timepoint at which the status of the job has changed
* ‘status’ – Possible values are QUEUED, ACTIVE, FINISHED, WAITING, REJECTED,
UNKNOWN JOBID or QUEUE DOWN

2. pollQueue [common]
Once obtained from ‘runService’, a job identification can be used to poll the
status to see if the result is ready for download.

Input: [common]
* ‘jobid’ – The 32 byte identification string of the job
Output: [common]
* ‘jobid’ – The 32 byte identification string of the job
* ‘datetime’ – The last timepoint at which the status of the job has changed
* ‘status’ – Possible values are QUEUED, ACTIVE, FINISHED, WAITING, REJECTED,
UNKNOWN JOBID or QUEUE DOWN

3. fetchResult [distinct/common]
Once the status is ‘FINISHED’ the results generated by the Web Service can be retrieved by
specifying the jobid;

Input: [common]
* ‘jobid’ – The 32 byte identification string of the job
Output: [distinct]
* ‘predictionTitle’ – Short description of the generated output
* ‘predictor’ – Name and version of the program which generated the output
* ‘predictionDate’ – Date at the time the when the prediction finished
* ‘entries’ – A collection of gene predictions containing the following information:
* ‘mol’ – Molecule type (5/8s, 16/18s, or 23/28s rRNA)
* ‘feature’ – feature type (rRNA)
* ‘start’ – Start position of the gene (integer)
* ‘stop’ – stop position of the gene (integer)
* ‘direction’ – strand of the gene (+/-)
* ‘score’ – The HMM alignment score (floating point number)
* ‘evalue’ – The E-value of the HMM alignment (floating point number)
* ‘sequenceEntry’ – The sequence identifier ( as specified when sequence
was uploaded )
* ‘sequence’ – The gene sequence extracted from the genomic contig
* ‘model_string’ – The consensus of the Hidden Markov Model (output from hmmsearch)
* ‘match_string’ – The match of the query to the model (output from hmmsearch)
* ‘query_string’ – The query sequence (output from hmmsearch)

For more information, please contact Peter F. Hallin: pfh@cbs.dtu.dk

The method is described in the following paper:
RNAmmer: consistent and rapid annotation of ribosomal RNA genes (2007) Karin Lagesen, Peter Fischer Hallin,
and David W. Ussery

Name
RNAmmer
Documentation
http://www.cbs.dtu.dk/ws/RNAmmer
Protocol
SOAP
WSDL
Endpoint
http://ws.cbs.dtu.dk:80/cgi-bin/soap/ws/quasi.cgi
Topic
Biology
Type
Tags
, , , , , , , , , ,
Description

This Web Service predicts location of ribosomal RNA genes in full genome sequences by using Hidden Markov Models based on [...]

Further information

This Web Service predicts location of ribosomal RNA genes in full genome sequences
by using Hidden Markov Models based on alignments from a highly cureated dataset of
structurally aligned sequnces.

The input is one or more genomic sequence(s) as either one or more contigs. Each contig
is submitted as one continous string of DNA together with the sequences identifier.

The kingdom (either Bacteria, Archaea, or Eukaryotes) is specified once for each job
that is submitted, using the abbriviations ‘bac’, ‘arc’, and ‘euk’.

More information about the method can be found at:

http://www.cbs.dtu.dk/services/RNAmmer/

This service is fully asynchronous; the usage is split into the following
three operations, which is usually executed in this order.

Procedures and messages used are either common and shared among all the CBS
Web Services, or distinct to each individual Web Service. Marked [distinct] and
[common] respectively.

1. runService [distinct/common]
Submit the input parapeter(s) and sequence data and returns a job identifier

Input: [distinct]
* ‘mol’ -Molecule (e.g. ssu,lsu,tsu)
* ‘kingdom’ – The kingdom of the genomic sequence
3 kingdoms are available: bac, euk, arc. This is specified
only once for the sequences in the current job.
* ‘sequences’ – An array of sequence objects, containing the following elements:
* ‘ident’ – The identifier of the sequence
* ‘seq’ – The sequence specified as one continous string
Output: [common]
* ‘jobid’ – The 32 byte identification string of the job
* ‘datetime’ – The last timepoint at which the status of the job has changed
* ‘status’ – Possible values are QUEUED, ACTIVE, FINISHED, WAITING, REJECTED,
UNKNOWN JOBID or QUEUE DOWN

2. pollQueue [common]
Once obtained from ‘runService’, a job identification can be used to poll the
status to see if the result is ready for download.

Input: [common]
* ‘jobid’ – The 32 byte identification string of the job
Output: [common]
* ‘jobid’ – The 32 byte identification string of the job
* ‘datetime’ – The last timepoint at which the status of the job has changed
* ‘status’ – Possible values are QUEUED, ACTIVE, FINISHED, WAITING, REJECTED,
UNKNOWN JOBID or QUEUE DOWN

3. fetchResult [distinct/common]
Once the status is ‘FINISHED’ the results generated by the Web Service can be retrieved by
specifying the jobid;

Input: [common]
* ‘jobid’ – The 32 byte identification string of the job
Output: [distinct]
* ‘predictionTitle’ – Short description of the generated output
* ‘predictor’ – Name and version of the program which generated the output
* ‘predictionDate’ – Date at the time the when the prediction finished
* ‘entries’ – A collection of gene predictions containing the following information:
* ‘mol’ – Molecule type (5/8s, 16/18s, or 23/28s rRNA)
* ‘feature’ – feature type (rRNA)
* ‘start’ – Start position of the gene (integer)
* ‘stop’ – stop position of the gene (integer)
* ‘direction’ – strand of the gene (+/-)
* ‘score’ – The HMM alignment score (floating point number)
* ‘evalue’ – The E-value of the HMM alignment (floating point number)
* ‘sequenceEntry’ – The sequence identifier ( as specified when sequence
was uploaded )
* ‘sequence’ – The gene sequence extracted from the genomic contig
* ‘model_string’ – The consensus of the Hidden Markov Model (output from hmmsearch)
* ‘match_string’ – The match of the query to the model (output from hmmsearch)
* ‘query_string’ – The query sequence (output from hmmsearch)

For more information, please contact Peter F. Hallin: pfh@cbs.dtu.dk

The method is described in the following paper:
RNAmmer: consistent and rapid annotation of ribosomal RNA genes (2007) Karin Lagesen, Peter Fischer Hallin,
and David W. Ussery

Original source
BioCatalogue

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