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Bioinformatics Advance Access originally published online on March 4, 2004
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Bioinformatics 20(11) © Oxford University Press 2004; all rights reserved.

Applications Note

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

Peter M. Haverty 1 and Zhiping Weng 1,2,*

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

Received on December 31, 2003; revised on February 18, 2004; accepted on February 20, 2004
Advance Access Publication March 4, 2004

Summary: CisML is an XML-based 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 the sample output.

Contact: zhiping{at}bu.edu

* To whom correspondence should be addressed.


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