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Chromhome: A rich internet application for accessing comparative chromosome homology maps
BACKGROUND: Comparative genomics has become a significant research area in recent years, following the availability of a number of sequenced genomes. The comparison of genomes is of great importance in the analysis of functionally important genome regions. It can also be used to understand the phylo...
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Formato: | Texto |
Lenguaje: | English |
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BioMed Central
2008
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323974/ https://www.ncbi.nlm.nih.gov/pubmed/18366796 http://dx.doi.org/10.1186/1471-2105-9-168 |
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author | Nagarajan, Sridevi Rens, Willem Stalker, James Cox, Tony Ferguson-Smith, Malcolm A |
author_facet | Nagarajan, Sridevi Rens, Willem Stalker, James Cox, Tony Ferguson-Smith, Malcolm A |
author_sort | Nagarajan, Sridevi |
collection | PubMed |
description | BACKGROUND: Comparative genomics has become a significant research area in recent years, following the availability of a number of sequenced genomes. The comparison of genomes is of great importance in the analysis of functionally important genome regions. It can also be used to understand the phylogenetic relationships of species and the mechanisms leading to rearrangement of karyotypes during evolution. Many species have been studied at the cytogenetic level by cross species chromosome painting. With the large amount of such information, it has become vital to computerize the data and make them accessible worldwide. Chromhome is a comprehensive web application that is designed to provide cytogenetic comparisons among species and to fulfil this need. RESULTS: The Chromhome application architecture is multi-tiered with an interactive client layer, business logic and database layers. Enterprise java platform with open source framework OpenLaszlo is used to implement the Rich Internet Chromhome Application. Cross species comparative mapping raw data are collected and the processed information is stored into MySQL Chromhome database. Chromhome Release 1.0 contains 109 homology maps from 51 species. The data cover species from 14 orders and 30 families. The homology map displays all the chromosomes of the compared species as one image, making comparisons among species easier. Inferred data also provides maps of homologous regions that could serve as a guideline for researchers involved in phylogenetic or evolution based studies. CONCLUSION: Chromhome provides a useful resource for comparative genomics, holding graphical homology maps of a wide range of species. It brings together cytogenetic data of many genomes under one roof. Inferred painting can often determine the chromosomal homologous regions between two species, if each has been compared with a common third species. Inferred painting greatly reduces the need to map entire genomes and helps focus only on relevant regions of the chromosomes of the species under study. Future releases of Chromhome will accommodate more species and their respective gene and BAC maps, in addition to chromosome painting data. Chromhome application provides a single-page interface (SPI) with desktop style layout, delivering a better and richer user experience. |
format | Text |
id | pubmed-2323974 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2008 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-23239742008-04-22 Chromhome: A rich internet application for accessing comparative chromosome homology maps Nagarajan, Sridevi Rens, Willem Stalker, James Cox, Tony Ferguson-Smith, Malcolm A BMC Bioinformatics Software BACKGROUND: Comparative genomics has become a significant research area in recent years, following the availability of a number of sequenced genomes. The comparison of genomes is of great importance in the analysis of functionally important genome regions. It can also be used to understand the phylogenetic relationships of species and the mechanisms leading to rearrangement of karyotypes during evolution. Many species have been studied at the cytogenetic level by cross species chromosome painting. With the large amount of such information, it has become vital to computerize the data and make them accessible worldwide. Chromhome is a comprehensive web application that is designed to provide cytogenetic comparisons among species and to fulfil this need. RESULTS: The Chromhome application architecture is multi-tiered with an interactive client layer, business logic and database layers. Enterprise java platform with open source framework OpenLaszlo is used to implement the Rich Internet Chromhome Application. Cross species comparative mapping raw data are collected and the processed information is stored into MySQL Chromhome database. Chromhome Release 1.0 contains 109 homology maps from 51 species. The data cover species from 14 orders and 30 families. The homology map displays all the chromosomes of the compared species as one image, making comparisons among species easier. Inferred data also provides maps of homologous regions that could serve as a guideline for researchers involved in phylogenetic or evolution based studies. CONCLUSION: Chromhome provides a useful resource for comparative genomics, holding graphical homology maps of a wide range of species. It brings together cytogenetic data of many genomes under one roof. Inferred painting can often determine the chromosomal homologous regions between two species, if each has been compared with a common third species. Inferred painting greatly reduces the need to map entire genomes and helps focus only on relevant regions of the chromosomes of the species under study. Future releases of Chromhome will accommodate more species and their respective gene and BAC maps, in addition to chromosome painting data. Chromhome application provides a single-page interface (SPI) with desktop style layout, delivering a better and richer user experience. BioMed Central 2008-03-26 /pmc/articles/PMC2323974/ /pubmed/18366796 http://dx.doi.org/10.1186/1471-2105-9-168 Text en Copyright © 2008 Nagarajan et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License ( (http://creativecommons.org/licenses/by/2.0) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Software Nagarajan, Sridevi Rens, Willem Stalker, James Cox, Tony Ferguson-Smith, Malcolm A Chromhome: A rich internet application for accessing comparative chromosome homology maps |
title | Chromhome: A rich internet application for accessing comparative chromosome homology maps |
title_full | Chromhome: A rich internet application for accessing comparative chromosome homology maps |
title_fullStr | Chromhome: A rich internet application for accessing comparative chromosome homology maps |
title_full_unstemmed | Chromhome: A rich internet application for accessing comparative chromosome homology maps |
title_short | Chromhome: A rich internet application for accessing comparative chromosome homology maps |
title_sort | chromhome: a rich internet application for accessing comparative chromosome homology maps |
topic | Software |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2323974/ https://www.ncbi.nlm.nih.gov/pubmed/18366796 http://dx.doi.org/10.1186/1471-2105-9-168 |
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