Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W56-64.

Dcode.org anthology of comparative genomic tools.

Source

Genome Biology Division, Lawrence Livermore National Laboratory, 7000 East Avenue, L-441 Livermore, CA 94550, USA.

Abstract

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 http://www.dcode.org/ website.

PMID:: 15980535; [PubMed - indexed for MEDLINE]
PMCID:: PMC1160116

Free PMC Article

Images from this publication.See all images (5) Free text

Publication Types, MeSH Terms, Substances

Publication Types

Research Support, U.S. Gov't, Non-P.H.S.

MeSH Terms

Substances

Transcription Factors

LinkOut - more resources

Full Text Sources

Other Literature Sources

COS Scholar Universe

Molecular Biology Databases

DCODE.ORG - Bioinformatics.ca Links Directory

Supplemental Content

Save items

Related citations in PubMed

Mulan: multiple-sequence local alignment and visualization for studying function and evolution. [Genome Res. 2005]
Mulan: multiple-sequence local alignment and visualization for studying function and evolution.
Ovcharenko I, Loots GG, Giardine BM, Hou M, Ma J, Hardison RC, Stubbs L, Miller W. Genome Res. 2005 Jan; 15(1):184-94. Epub 2004 Dec 8.
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes. [Nucleic Acids Res. 2004]
ECR Browser: a tool for visualizing and accessing data from comparisons of multiple vertebrate genomes.
Ovcharenko I, Nobrega MA, Loots GG, Stubbs L. Nucleic Acids Res. 2004 Jul 1; 32(Web Server issue):W280-6.
rVISTA 2.0: evolutionary analysis of transcription factor binding sites. [Nucleic Acids Res. 2004]
rVISTA 2.0: evolutionary analysis of transcription factor binding sites.
Loots GG, Ovcharenko I. Nucleic Acids Res. 2004 Jul 1; 32(Web Server issue):W217-21.
Review The identification and functional characterisation of conserved regulatory elements in developmental genes. [Brief Funct Genomic Proteomic....]
Review The identification and functional characterisation of conserved regulatory elements in developmental genes.
Dickmeis T, Müller F. Brief Funct Genomic Proteomic. 2005 Feb; 3(4):332-50.
Review Comparative and evolutionary genomics of globin genes in fish. [Methods Enzymol. 2008]
Review Comparative and evolutionary genomics of globin genes in fish.
Negrisolo E, Bargelloni L, Patarnello T, Ozouf-Costaz C, Pisano E, di Prisco G, Verde C. Methods Enzymol. 2008; 436:511-38.

See reviews... See all...

Cited by 13 PubMed Central articles

Comparative analysis of the ATRX promoter and 5' regulatory region reveals conserved regulatory elements which are linked to roles in neurodevelopment, alpha-globin regulation and testicular function. [BMC Res Notes. 2011]
Comparative analysis of the ATRX promoter and 5' regulatory region reveals conserved regulatory elements which are linked to roles in neurodevelopment, alpha-globin regulation and testicular function.
Tang P, Frankenberg S, Argentaro A, Graves JM, Familari M. BMC Res Notes. 2011 Jun 15; 4:200. Epub 2011 Jun 15.
Conserved proximal promoter elements control repulsive guidance molecule c/hemojuvelin (Hfe2) gene transcription in skeletal muscle. [Genomics. 2010]
Conserved proximal promoter elements control repulsive guidance molecule c/hemojuvelin (Hfe2) gene transcription in skeletal muscle.
Severyn CJ, Rotwein P. Genomics. 2010 Dec; 96(6):342-51. Epub 2010 Sep 19.
AhR-mediated gene expression in the developing mouse telencephalon. [Reprod Toxicol. 2009]
AhR-mediated gene expression in the developing mouse telencephalon.
Gohlke JM, Stockton PS, Sieber S, Foley J, Portier CJ. Reprod Toxicol. 2009 Nov; 28(3):321-8. Epub 2009 May 22.

See all...

Related information

Related Citations
Calculated set of PubMed citations closely related to the selected article(s) retrieved using a word weight algorithm. Related articles are displayed in ranked order from most to least relevant, with the “linked from” citation displayed first.
References for this PMC Article
Citation referenced in PubMed article. Only valid for PubMed citations that are also in PMC.
Free in PMC
Free full text articles in PMC
Cited in PMC
Full-text articles in the PubMed Central Database that cite the current articles.

Recent activity

Clear Turn Off Turn On

Dcode.org anthology of comparative genomic tools.
Dcode.org anthology of comparative genomic tools.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W56-64.

PubMed
POWER: PhylOgenetic WEb Repeater--an integrated and user-optimized framework for...
POWER: PhylOgenetic WEb Repeater--an integrated and user-optimized framework for biomolecular phylogenetic analysis.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W553-6.

PubMed
PriFi: using a multiple alignment of related sequences to find primers for ampli...
PriFi: using a multiple alignment of related sequences to find primers for amplification of homologs.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W516-20.

PubMed
MICheck: a web tool for fast checking of syntactic annotations of bacterial geno...
MICheck: a web tool for fast checking of syntactic annotations of bacterial genomes.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W471-9.

PubMed
BABELOMICS: a suite of web tools for functional annotation and analysis of group...
BABELOMICS: a suite of web tools for functional annotation and analysis of groups of genes in high-throughput experiments.
Nucleic Acids Res. 2005 Jul 1 ;33(Web Server issue):W460-4.

PubMed

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

PubMed

Result Filters

Display Settings:

Send to: