| Info. | Vol.5 - No.3 (2011.09.20) |
|---|---|
| Title | CNVAS: Copy Number Variation Analysis System - The analysis tool for genomic alteration with a powerful visualization module |
| Authors | Jinho Yoo1, In Cheol Ha1, Gyu Tae Chang2, Kwang Su Jung3, Kiejung Park3 & Yangseok Kim4 |
| Institutions | 1Bioinformatics Unit, ISTECH Inc. No. 402, Jipyung Plaza B/D, 863 Janghang2-dong, Ilsandong-gu, Goyang-si, Gyeonggi-do 410-837,Korea 2Department of Oriental Pediatrics, College of Oriental Medicine, Kyung Hee University, #1 Hoeki-dong, Dongdaemun-gu, Seoul 130-701, Korea 3Division of Bio-Medical Informatics, Center for Genome Science, Korea National Institution of Health, 187 Osongsaengmyeong2(i)-ro, Gangoe-myeon, Cheongwon-gun, Chungcheongbuk-do 363-951, Korea 4Department of Physiology, College of Oriental Medicine, Kyung Hee University, #1 Hoeki-dong, Dongdaemun-gu, Seoul 130-701, Korea Correspondence and requests for materials should be addressed to K. Park ( kjpark63@gmail.com) and Y. Kim ( yskim1158@khu.ac.kr) |
| Abstract | Recently, Copy Number Variation (CNV) has been recognized as one of the most important genomic alterations in the study of human variation, as it can be employed as a novel marker for human disease studies. Thus, many hardware technologies have been developed to detect copy number variations, including chip-based technologies. However, owing to its complexity, relatively few analysis tools are currently available for CNV, and most public tools have only limited functions and Graphic User Interfaces (GUI). CNVAS is a powerful software package for the analysis of CNV. Two different algorithms, Smith Waterman (SW) and Circular Binary Segmentation (CBS), are implemented for the detection of CNV regions. Furthermore, in order to evaluate the relationship between phenotype and CNV, CNVAS can perform the Chi-square test and Fisher?셲 exact test. Result visualization is another strong merit of the CNVAS software. CNVAS can show the analysis results in the form of chromosome ideograms, and these can be exported in the form of an image file. Furthermore, CNVAS has a database system, which can manage the user?셲 data from different sources and under different experimental conditions. CNVAS is a web-based program, and users can freely access the CNVAS by connecting to http://biomi.cdc.go.kr/CNVAS/. |
| Keyword | Copy Number Variation, Phenotype-specific CNV, Bioinformatics, Chromosome visualization, Association study |
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