Skip Navigation



Bioinformatics Advance Access published online on July 5, 2005
Bioinformatics, doi:10.1093/bioinformatics/bti566
This Article
Right arrow Advance Access manuscript (PDF) Freely available
Right arrow All Versions of this Article:
21/17/3469    most recent
bti566v1
Right arrow Comments: Submit a response
Right arrow Alert me when this article is cited
Right arrow Alert me when Comments are posted
Right arrow Alert me if a correction is posted
Services
Right arrow Email this article to a friend
Right arrow Similar articles in this journal
Right arrow Similar articles in PubMed
Right arrow Alert me to new issues of the journal
Right arrow Add to My Personal Archive
Right arrow Download to citation manager
Right arrowRequest Permissions
Google Scholar
Right arrow Articles by Yen, K.-H.
Right arrow Articles by Ho, C.-L.
Right arrow Search for Related Content
PubMed
Right arrow PubMed Citation
Right arrow Articles by Yen, K.-H.
Right arrow Articles by Ho, C.-L.
Social Bookmarking
Add to CiteULike   Add to Connotea   Add to Del.icio.us  
What's this?

© The Author (2005). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oupjournals.org
Received November 26, 2004
Revised June 28, 2005
Accepted June 28, 2005

Article

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

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

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

* To whom correspondence should be addressed.
Chung-Liang Ho, E-mail: moris{at}dblab.csie.ncku.edu.tw; clh9@mail.ncku.edu.tw


  Abstract

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 database, making it possible to find all genes in the disease-related cytobands through database query. However, finding genes in cytobands remains to be an imprecise process, partly due to the insufficiency of current methods for cytoband query, 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 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/.

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


Add to CiteULike CiteULike   Add to Connotea Connotea   Add to Del.icio.us Del.icio.us    What's this?


This article has been cited by other articles:


Home page
 BioinformaticsHome page
K.-H. Yen, C.-L. Ho, and C. Lee
The analysis of inconsistencies between cytogenetic annotations and sequence mapping by defining the imprecision zones of cytogenetic banding
Bioinformatics, April 1, 2009; 25(7): 845 - 852.
[Abstract] [Full Text] [PDF]


Disclaimer: Please note that abstracts for content published before 1996 were created through digital scanning and may therefore not exactly replicate the text of the original print issues. All efforts have been made to ensure accuracy, but the Publisher will not be held responsible for any remaining inaccuracies. If you require any further clarification, please contact our Customer Services Department.