NCBI Dcode.org Comparative Genomics Developments :: News

April 30, 2008 The DiRE tool operates with new ECR Browser alignments now. It is also possible to run DiRE on human (hg18), mouse (mm9), and rat (rn4) genomes. April 16, 2008 New ECR Browser alignments and TRANSFAC library updates have been propagated into ECRbase and SynoR tools. DiRE databases of conserved transcription factor binding sites are expected to be updated by the end of the month. March 4, 2008 120+ new vertebrate genome alignments (with repeats included) now available in ECR Browser February 1, 2008 New version of ECR Browser (http://ecrbrowser.dcode.org/)   - multiple gene annotation tracks   - possibility to submit your own custom genome annotation   - share your cussom annotation by submitting it to        the ECR Browser User Annotation Database   - enhanced search through RefSeq, UCSC, Ensembl, mRNA, STS, SNPs, etc.   - zoom in/out using mouse wheel (similar to Google Maps)   - drag & drop rearrangement of gene annotation tracks   - drag & drop recentering of the conservation plot   - gene annotation drop on the conservation plot changes the reference annotation   - new alignments with repetitive elements included (colored in green)   - on-the-fly ECR and gene annotation   - keyboard shortcuts ( o - zoom out 3x,  i - zoom in 3x,  > - shift to the right, ...) etc, etc... December 22, 2007  Add ECR Browser search button to your Google Toolbar. Click HERE and select your favorite genome. (You might need Administrative priviledges to complete the installation.) December 15, 2007 DCODE.org web site has been moved to the Computational Biology Branch of the National Center for Biotechnology Information (NCBI) at NIH/NLM. It is now called NCBI DCODE.org Comparative Genomics Developments. Stable hardware architecture, high-performance computers, and significantly increased storage capabilities ensure timely updates, 100% availability, and faster response time. Many thanks to Dima Beloslyudtsev, John S.J. Anderson, Steven Feehan, Jim Fleshman, Don Preuss, and David Landsman from NCBI for making this possible and for all the hard work! November 5, 2007 Release of a new tool :: DiRE (http://dire.dcode.org) DiRE is a web server for identification of proximal and Distant Regulatory Elements (enhancers, repressors, etc) and candidate regulatory transcription factors in loci of co-regulated genes. January 8, 2007    "Predicting tissue-specific enhancers in the human genome" manuscript that describes a novel method to translate co-expression data into sets of distant and proximal gene regulatory elements was published online in Genome Research [PDF].    Details are here. November 7, 2006    "ECRbase: Database of Evolutionary Conserved Regions, Promoters, and Transcription Factor Binding Sites in Vertebrate Genomes" manuscript describing a new Dcode.org resource was published in Bioinformatics [PDF]. October 10, 2006    Updated version of conserved transcription factor binding sites (TRANSFAC Prof V10.2) is available in ECR Browser for the human and mouse genomes in alignments with mouse/human, chicken, frog, and fugu genomes. October 10, 2006    TRANSFAC Prof V10.2 matrices are available in rVista 2.0 October 6, 2006    Chicken (galGal3; August 06; v2.1) genome was added to the ECR Browser. August 29, 2006    New resource available at Dcode.org.    ECRbase (http://ecrbase.dcode.org) is the database of evolutionary conserved regions, promoters, and transcription factor binding sites in vertebrate genomes created using ECR Browser alignments. July 26, 2006    Opossum (monDom1) and Rhesus macaque (rheMac2) alignments are available for the human genome in ECR Browser. July 11, 2006    Rat (v3.4 June 2006) ECR Browser released. Multiple genome alignments including rat-mouse. July 5, 2006    The list of genomes that can be automatically fetched from UCSC Genome Browser in zPicture and Mulan was expanded and updated to the latest genome assemblies. It now includes human, chimp, rhesus, dog, cow, mouse, rat, opossum, chicken, frog, z-fish, tetraodon, and fugu fish. July 3, 2006    Identification of SNPs in conserved elements option is active in the Human ECR Browser. June 19, 2006    - Many new genomes and genome alignments are available in ECR Browser:       -- Human (March 2006; hg18);       -- Mouse (February 2006; mm8);       -- Dog (May 2005; canFam2);       -- Xenopus tropicalis (August 2005; v4.1);       -- Zebrafish (Zv6);       -- Fugu (October 2004; v4.0). June 16, 2006    - "Array2BIO: from microarray expression data to functional annotation of co-regulated genes" was published in BMC Bioinformatics December 1, 2005    - Array2BIO - a freely available suite of utilities for the analysis of microarray data was added to the Dcode.org toolbox. August 16, 2005    - rVista 2.0 modifications: (a) an option to generate "smooth-plots" was added, (b) new "individual clustering" method. July 26, 2005    - The newest TBA aligner was incorporated into Mulan. Now Mulan is capable of handling duplications in multiple-sequence alignments. July 14, 2005    - Bioinformatics postdoctoral position opening to work as a member of the Dcode.org team. July 1, 2005 - SynoR and Dcode.org utilities were described in the web-tools special issue of the Nucleic Acids Research journal. It includes the interactive whole genome annotation of multi-species conserved TFBS available from the ECR Browser. June 7, 2005 - Dcode.org collection of tools was featured in the Science and Technology Review LLNL's magazine. May 20, 2005 - SynoR program was developed to scan vertebrate genomes for specific clusters of conserved TFBS. May 12, 2005 - Redesigned DCODE.org web site is launched. - Forum option is introduced to promote communication inside the comparative genomics community. - EurekAlert! Bioinformatics News section is added. RSS