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Dcode.org anthology of comparative genomic tools

Comparative genomics provides the means to demarcate functional regions in anonymous DNA sequences. The successful application of this method to identifying novel genes is currently shifting to deciphering the non-coding encryption of gene regulation across genomes. To facilitate the practical appli...

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Detalles Bibliográficos
Autores principales: Loots, Gabriela G., Ovcharenko, Ivan
Formato: Texto
Lenguaje:English
Publicado: Oxford University Press 2005
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160116/
https://www.ncbi.nlm.nih.gov/pubmed/15980535
http://dx.doi.org/10.1093/nar/gki355
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author Loots, Gabriela G.
Ovcharenko, Ivan
author_facet Loots, Gabriela G.
Ovcharenko, Ivan
author_sort Loots, Gabriela G.
collection PubMed
description Comparative genomics provides the means to demarcate functional regions in anonymous DNA sequences. The successful application of this method to identifying novel genes is currently shifting to deciphering the non-coding encryption of gene regulation across genomes. To facilitate the practical application of comparative sequence analysis to genetics and genomics, we have developed several analytical and visualization tools for the analysis of arbitrary sequences and whole genomes. These tools include two alignment tools, zPicture and Mulan; a phylogenetic shadowing tool, eShadow for identifying lineage- and species-specific functional elements; two evolutionary conserved transcription factor analysis tools, rVista and multiTF; a tool for extracting cis-regulatory modules governing the expression of co-regulated genes, Creme 2.0; and a dynamic portal to multiple vertebrate and invertebrate genome alignments, the ECR Browser. Here, we briefly describe each one of these tools and provide specific examples on their practical applications. All the tools are publicly available at the website.
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spelling pubmed-11601162005-06-29 Dcode.org anthology of comparative genomic tools Loots, Gabriela G. Ovcharenko, Ivan Nucleic Acids Res Article Comparative genomics provides the means to demarcate functional regions in anonymous DNA sequences. The successful application of this method to identifying novel genes is currently shifting to deciphering the non-coding encryption of gene regulation across genomes. To facilitate the practical application of comparative sequence analysis to genetics and genomics, we have developed several analytical and visualization tools for the analysis of arbitrary sequences and whole genomes. These tools include two alignment tools, zPicture and Mulan; a phylogenetic shadowing tool, eShadow for identifying lineage- and species-specific functional elements; two evolutionary conserved transcription factor analysis tools, rVista and multiTF; a tool for extracting cis-regulatory modules governing the expression of co-regulated genes, Creme 2.0; and a dynamic portal to multiple vertebrate and invertebrate genome alignments, the ECR Browser. Here, we briefly describe each one of these tools and provide specific examples on their practical applications. All the tools are publicly available at the website. Oxford University Press 2005-07-01 2005-06-27 /pmc/articles/PMC1160116/ /pubmed/15980535 http://dx.doi.org/10.1093/nar/gki355 Text en © The Author 2005. Published by Oxford University Press. All rights reserved
spellingShingle Article
Loots, Gabriela G.
Ovcharenko, Ivan
Dcode.org anthology of comparative genomic tools
title Dcode.org anthology of comparative genomic tools
title_full Dcode.org anthology of comparative genomic tools
title_fullStr Dcode.org anthology of comparative genomic tools
title_full_unstemmed Dcode.org anthology of comparative genomic tools
title_short Dcode.org anthology of comparative genomic tools
title_sort dcode.org anthology of comparative genomic tools
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160116/
https://www.ncbi.nlm.nih.gov/pubmed/15980535
http://dx.doi.org/10.1093/nar/gki355
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