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 noncoding encryption of gene regulation across genomes. To facilitate the use of comparative genomics to practical applications in 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; 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/ web site.
- Research Organization:
- Lawrence Livermore National Laboratory (LLNL), Livermore, CA
- Sponsoring Organization:
- USDOE
- DOE Contract Number:
- W-7405-ENG-48
- OSTI ID:
- 15017386
- Report Number(s):
- UCRL-JRNL-209160
- Journal Information:
- Nucleic Acids Research, Journal Name: Nucleic Acids Research Vol. 33
- Country of Publication:
- United States
- Language:
- English
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ECR Browser: A Tool For Visualizing And Accessing Data From Comparisons Of Multiple Vertebrate Genomes
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