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Bioinformatics Advance Access published online on March 4, 2004
Bioinformatics, doi:10.1093/bioinformatics/bth162
Bioinformatics © Oxford University Press 2004; all rights reserved
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Received December 31, 2003
Revised February 18, 2004
Accepted February 20, 2004

Applications note

CisML: an XML-based output format for sequence motif detection software

Peter M. Haverty 1 Zhiping Weng 2*

1 1Bioinformatics Program, Boston University, Boston, MA 02215
2 1Bioinformatics Program, Boston University, Boston, MA 02215; 2Biomedical Engineering Department, Boston University, Boston, MA 02215

* To whom correspondence should be addressed. E-mail: zhiping{at}bu.edu.


  Abstract

Summary: CisML is an XML-based output format for sequence motif detection software. This proposed standard is applicable to many types of sequence motif detection programs. It is intended to facilitate the integration of data and the comparison of results from different software packages, and to simplify the development of downstream tools. XSL stylesheets are provided for easy generation of text, html and graphical reports from CisML-formatted data.

Availability: http://zlab.bu.edu/CisML/.

Supplementary Information: Example CisML-formatted data and XSL stylesheets for report generation are available along with sample output.


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