SeeGH – A software tool for visualization of whole genome array comparative genomic hybridization data
<p>Abstract</p> <p>Background</p> <p>Array comparative genomic hybridization (CGH) is a technique which detects copy number differences in DNA segments. Complete sequencing of the human genome and the development of an array representing a tiling set of tens of thousand...
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| Format: | Article |
| Language: | English |
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BMC
2004-02-01
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| Series: | BMC Bioinformatics |
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| Online Access: | http://www.biomedcentral.com/1471-2105/5/13 |
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| author | MacAulay Calum Coe Bradley P deLeeuw Ronald J Chi Bryan Lam Wan L |
| author_facet | MacAulay Calum Coe Bradley P deLeeuw Ronald J Chi Bryan Lam Wan L |
| author_sort | MacAulay Calum |
| collection | DOAJ |
| description | <p>Abstract</p> <p>Background</p> <p>Array comparative genomic hybridization (CGH) is a technique which detects copy number differences in DNA segments. Complete sequencing of the human genome and the development of an array representing a tiling set of tens of thousands of DNA segments spanning the entire human genome has made high resolution copy number analysis throughout the genome possible. Since array CGH provides signal ratio for each DNA segment, visualization would require the reassembly of individual data points into chromosome profiles.</p> <p>Results</p> <p>We have developed a visualization tool for displaying whole genome array CGH data in the context of chromosomal location. SeeGH is an application that translates spot signal ratio data from array CGH experiments to displays of high resolution chromosome profiles. Data is imported from a simple tab delimited text file obtained from standard microarray image analysis software. SeeGH processes the signal ratio data and graphically displays it in a conventional CGH karyotype diagram with the added features of magnification and DNA segment annotation. In this process, SeeGH imports the data into a database, calculates the average ratio and standard deviation for each replicate spot, and links them to chromosome regions for graphical display. Once the data is displayed, users have the option of hiding or flagging DNA segments based on user defined criteria, and retrieve annotation information such as clone name, NCBI sequence accession number, ratio, base pair position on the chromosome, and standard deviation.</p> <p>Conclusions</p> <p>SeeGH represents a novel software tool used to view and analyze array CGH data. The software gives users the ability to view the data in an overall genomic view as well as magnify specific chromosomal regions facilitating the precise localization of genetic alterations. SeeGH is easily installed and runs on Microsoft Windows 2000 or later environments.</p> |
| first_indexed | 2024-12-21T13:43:57Z |
| format | Article |
| id | doaj.art-f87fa945c9534fc18eeb03b8cc253770 |
| institution | Directory Open Access Journal |
| issn | 1471-2105 |
| language | English |
| last_indexed | 2024-12-21T13:43:57Z |
| publishDate | 2004-02-01 |
| publisher | BMC |
| record_format | Article |
| series | BMC Bioinformatics |
| spelling | doaj.art-f87fa945c9534fc18eeb03b8cc2537702022-12-21T19:01:56ZengBMCBMC Bioinformatics1471-21052004-02-01511310.1186/1471-2105-5-13SeeGH – A software tool for visualization of whole genome array comparative genomic hybridization dataMacAulay CalumCoe Bradley PdeLeeuw Ronald JChi BryanLam Wan L<p>Abstract</p> <p>Background</p> <p>Array comparative genomic hybridization (CGH) is a technique which detects copy number differences in DNA segments. Complete sequencing of the human genome and the development of an array representing a tiling set of tens of thousands of DNA segments spanning the entire human genome has made high resolution copy number analysis throughout the genome possible. Since array CGH provides signal ratio for each DNA segment, visualization would require the reassembly of individual data points into chromosome profiles.</p> <p>Results</p> <p>We have developed a visualization tool for displaying whole genome array CGH data in the context of chromosomal location. SeeGH is an application that translates spot signal ratio data from array CGH experiments to displays of high resolution chromosome profiles. Data is imported from a simple tab delimited text file obtained from standard microarray image analysis software. SeeGH processes the signal ratio data and graphically displays it in a conventional CGH karyotype diagram with the added features of magnification and DNA segment annotation. In this process, SeeGH imports the data into a database, calculates the average ratio and standard deviation for each replicate spot, and links them to chromosome regions for graphical display. Once the data is displayed, users have the option of hiding or flagging DNA segments based on user defined criteria, and retrieve annotation information such as clone name, NCBI sequence accession number, ratio, base pair position on the chromosome, and standard deviation.</p> <p>Conclusions</p> <p>SeeGH represents a novel software tool used to view and analyze array CGH data. The software gives users the ability to view the data in an overall genomic view as well as magnify specific chromosomal regions facilitating the precise localization of genetic alterations. SeeGH is easily installed and runs on Microsoft Windows 2000 or later environments.</p>http://www.biomedcentral.com/1471-2105/5/13Array comparitve genomic hybridizationaCGH |
| spellingShingle | MacAulay Calum Coe Bradley P deLeeuw Ronald J Chi Bryan Lam Wan L SeeGH – A software tool for visualization of whole genome array comparative genomic hybridization data BMC Bioinformatics Array comparitve genomic hybridization aCGH |
| title | SeeGH – A software tool for visualization of whole genome array comparative genomic hybridization data |
| title_full | SeeGH – A software tool for visualization of whole genome array comparative genomic hybridization data |
| title_fullStr | SeeGH – A software tool for visualization of whole genome array comparative genomic hybridization data |
| title_full_unstemmed | SeeGH – A software tool for visualization of whole genome array comparative genomic hybridization data |
| title_short | SeeGH – A software tool for visualization of whole genome array comparative genomic hybridization data |
| title_sort | seegh a software tool for visualization of whole genome array comparative genomic hybridization data |
| topic | Array comparitve genomic hybridization aCGH |
| url | http://www.biomedcentral.com/1471-2105/5/13 |
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