kcentroidfold

 

Function

Predicts RNA 2D structure using CentroidFold

Description

kcentroidfold predicts an RNA 2D structure from given RNA sequence utilizing CentroidFold. CentroidFold is based on the gamma-centroid estimator for high-dimensional discrete spaces.

kcentroidfold utilizes CentroidFold Web Server provided by ncRNA.org. Original web-service is located at the following URL:

http://www.ncrna.org/centroidfold/

This tools is a subset of Keio Bioinformatics Web Service (KBWS) package, which contains interfaces to bioinformatics web services through a proxy server at Keio University. kcentroidfold is thus an interface of "runCentroidFold" method included in KBWS SOAP service. This method can be alternatively accessed directly from programming languages as SOAP web service. Please refer to the KBWS online documentations http://soap.g-language.org/kbws/ for more information.

Usage


   Here is a sample session with kcentroidfold

% kcentroidfold
Predicts RNA 2D structure using CentroidFold
Input (gapped) sequence(s): test.fasta
Output file [55-110.centroidfold]: 
Jobid: kbws_12547145
***********

http://soap.g-language.org/alis/result/12547145.png

>M33000.1/55-110
ACGCUGUCUGUACUUGUAUCAGUACACUGACGAGUCCCUAAAGGACGAAACAGCGC
.(((((((((((((.(...)))))))..).(..((((.....)))))..)))))).

Command line arguments

Qualifier Type Description Allowed values Default
Standard (Mandatory) qualifiers
[-seqall]
(Parameter 1)		 seqall (Gapped) sequence(s) filename and optional format, or reference (input USA) Readable sequence(s) 2
[-outfile]
(Parameter 2)		 outfile Output file name Output file <*>.kcentroidfold
Additional (Optional) qualifiers
-model string information about this parameter Any string  
-gamma integer information about this parameter Any integer value 1024
Advanced (Unprompted) qualifiers
(none)

Input file format

kcentroidfold can use any genome sequence data that seqret can read.

Output file format

kcentroidfold outputs "Seq/Fold information" and "graph result". "Seq/Fold information" is general CentroidFold output file. "graph result" is an URL about image file of predicted 2D structure.

Data files

None.

Notes

None.

References


   Kengo, Sato., et al.,(2009) CentroidFold: a web server for RNA secondary
      structure prediction, Nucleic Acids Research, 37, 277-280.
   Michiaki, Hamada., et al.,(2009) Predictions of RNA secondary structure
      using generalized centroid estimators, Bioinformatics, 25(4), 465-473.

Warnings

None.

Diagnostic Error Messages

None.

Exit status

It always exits with a status of 0.

Known bugs

None.

See also

Program name Description
seqret Reads and writes (returns) sequences

Author(s)

Kazuki Oshita (cory @ g-language.org) Institute for Advanced Biosciences, Keio University 252-8520 Japan

History

2009 - Written by Kazuki Oshita

Target users

This program is intended to be used by everyone and everything, from naive users to embedded scripts.

Comments