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Bioinformatics Advance Access originally published online on July 5, 2005
Bioinformatics 2005 21(17):3469-3474; doi:10.1093/bioinformatics/bti566
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© The Author 2005. Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions{at}oupjournals.org

A precise and scalable method for querying genes in chromosomal banding regions based on cytogenetic annotations

Kuo-Ho Yen , Chiang Lee , Hsiao-Sheng Liu 1 and Chung-Liang Ho 2,3,*

Department of Computer Science and Information Engineering, National Cheng Kung University No 1. Da-Shueh Road Tainan, Taiwan
1Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University No 1. Da-Shueh Road Tainan, Taiwan
2Department of Pathology, National Cheng Kung University No 1. Da-Shueh Road Tainan, Taiwan
3Institute of Molecular Medicine, National Cheng Kung University No 1. Da-Shueh Road Tainan, Taiwan

*To whom correspondence should be addressed.

Motivation: Staining the human metaphase chromosomes reveals characteristic banding patterns known as cytogenetic bands or cytobands. Using technologies based on metaphase chromosomes, researchers have accumulated much knowledge about the correlations between human diseases and specific cytoband aberrations, indicating the presence of disease-associated genes in those bands. With the progress of human genome project and techniques such as fluorescent in situ hybridization, many genes have been assigned to the cytobands and annotated in public databases, making it possible to find all genes in the disease-related cytobands through database queries. However, finding genes in cytobands remains an imprecise process, partly due to the insufficiency of current methods for cytoband queries, especially for those based on cytogenetic annotations.

Results: By transforming the cytoband annotations into numerical segments, a new query method is developed that is able to accurately define any cytogenetic ranges in human chromosomes. A query system (designated cytoband query sys CQS) is implemented using cytogenetic annotations in the public domain. Judged by a performance test, CQS executed as accurately as expected using cytogenetic annotations from NCBI Map Viewer. The new method is scalable and can be applied to genomes from other species.

Availability: The CQS is freely accessible over the Internet at http://moris.csie.ncku.edu.tw/cqs/

Contact: clh9{at}mail.ncku.edu.tw

Supplementary information: http://moris.csie.ncku.edu.tw/cqs/

Received on November 26, 2004; revised on June 28, 2005; accepted on June 28, 2005

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