• chromosomes
  • This project continues our successful development of software for analyzing large molecular assemblies such as viruses, ribosomes, and chromosomes. (ucsf.edu)
  • Genome assembly refers to the process of taking a large number of short DNA sequences and putting them back together to create a representation of the original chromosomes from which the DNA originated. (wikipedia.org)
  • ARS Scientists in Albany have characterized switchgrass germplasm through controlled crosses and through analysis of mitotic chromosomes for the purposes of assigning unique identities to each chromosome and to align these with the genetic map. (usda.gov)
  • human
  • The Human Genome Project was a landmark genome project that is already having a major impact on research across the life sciences, with potential for spurring numerous medical and commercial developments. (wikipedia.org)
  • An example of such assembler Short Oligonucleotide Analysis Package developed by BGI for de novo assembly of human-sized genomes, alignment, SNP detection, resequencing, indel finding, and structural variation analysis. (wikipedia.org)
  • doi:10.1111/j.1399-3054.1982.tb00301.x. agmatinase at the US National Library of Medicine Medical Subject Headings (MeSH) Human AGMAT genome location and AGMAT gene details page in the UCSC Genome Browser. (wikipedia.org)
  • 2012). The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression. (springer.com)
  • Human ATP5G3 genome location and ATP5G3 gene details page in the UCSC Genome Browser. (wikipedia.org)
  • 2001: PANTHER 2 released, which is used in the annotationon of the first published human genome Celera. (wikipedia.org)
  • biology
  • Also, as scientists understand more about the role of this noncoding DNA (often referred to as junk DNA), it will become more important to have a complete genome sequence as a background to understanding the genetics and biology of any given organism. (wikipedia.org)
  • In 1972, Walter Fiers and his team at the Laboratory of Molecular Biology of the University of Ghent (Ghent, Belgium) were the first to determine the sequence of a gene: the gene for Bacteriophage MS2 coat protein. (wikipedia.org)
  • A good place to start a tour of molecular biology services on the WWW is the National Center for Biotechnology Information (NCBI, http://www.ncbi.nlm.nih.gov/ ). (virology.net)
  • GenBank at NCBI is part of the International Nucleotide Sequence Database Collaboration, in conjunction with the DNA DataBank of Japan (DDBJ, http://www.ddbj.nig.ac.jp/ ) and the European Molecular Biology Laboratory (EMBL, http://www.embl-heidelberg.de/ ). (virology.net)
  • thus
  • Thus we have identified a set of "driving biomedical research projects" (DBPs - listed below) that we are pursuing in collaboration with outside investigators. (ucsf.edu)
  • One approach to this is to actively engage the greater research community to collaborate, and thus we have identified several "collaboration and service projects" below as well. (ucsf.edu)
  • Thus, 'completed' genome sequences are rarely ever complete, and terms such as 'working draft' or 'essentially complete' have been used to more accurately describe the status of such genome projects. (wikipedia.org)
  • model organism
  • We are a founding member of the Alliance of Genome Resources, whose goal is to provide a consistent user interface with an integrated view of data from 6 Model Organism Databases and the GO Consortium. (jax.org)
  • PANTHER genomes set are selected based on the following criteria: The set should include a major experimental model organism, this will assist in depicting functional information of the organism which are less studied. (wikipedia.org)
  • structural
  • The Structure- Function Linkage Database (SFLD) is a resource designed to address difficult problems in linking sequence and structural information for divergent enzymes to their associated functions. (ucsf.edu)
  • Analysis of virion structural components reveals vestiges of the ancestral ichnovirus genome. (irisa.fr)
  • Here, we present genome-wide identification, structural and expression analyses of rice MT gene family. (springer.com)
  • data
  • Chimera has been used for visualizing molecular models (ranging in size from small molecules to virus capsids), molecular ensembles, and volumetric data. (ucsf.edu)
  • By providing a single extensible platform for applying analysis techniques and visually examining results in a facile manner, Chimera aids scientists in understanding their data and generating new hypotheses. (ucsf.edu)
  • It is used by hundreds of such labs, and is the primary software for visualization and analysis used by archivists at the public data repositories (PDB, EM Data Bank, VIPER Database). (ucsf.edu)
  • The prediction of protein function from structure or sequence data remains a problem best addressed by leveraging information available from previously determined structure-function relationships. (ucsf.edu)
  • bioinformaticist and software ingeneer at INRA's URGI laboratory (Versailles, France, leaded by Hadi Quesneville) in charge of the development and maintenance of annotation pipelines, physical mapping data management, web services, software maintenance and installation, projects support. (irisa.fr)
  • Outside of genome-based efforts, much of the data created in characterizing a specific gene is not relevant for this particular gene and is therefore often lost, even though it may become interesting for someone else later on. (genetics.org)
  • The IMAGE and MGI accession identifiers travel in pairs and are submitted to dbEST (database of Expressed Sequence Tags) directly with the sequencing data. (jax.org)
  • Golub says the team plans to increase its annotation of the cell lines in the collection, including proteomic and metabolic data, along with functional perturbations such as RNA interference screens. (aacrjournals.org)
  • This means that you type (or cut and paste) the sequence data directly into electronic fill-in-the-blank forms in the browser window, and then click a submit button. (virology.net)
  • These organizations exchange data daily and maintain nearly identical sequence databases. (virology.net)
  • These data types include mutant phenotypes, molecular characterization of mutant alleles and other deviations, cytological maps, wild-type expression patterns, anatomical images, transgenic constructs and insertions, sequence-level gene models and molecular classification of gene product functions. (wikipedia.org)
  • These groups recognized that most genome project and community data types overlapped. (wikipedia.org)
  • The goal of CGAP is to characterize cancer at a molecular level by providing a platform with readily accessible updated data and a set of tools such that researchers can easily relate their findings to existing knowledge. (wikipedia.org)
  • SAGE libraries have better read quality and generate a larger amount of data when sequenced, and since transcripts are compared in absolute rather than relative levels, SAGE has the advantage of requiring no normalisation of data via comparison with a reference. (wikipedia.org)
  • Following sequencing and establishment of libraries, CGAP incorporates the data along with existing data sources and provides various databases and tools for analysis. (wikipedia.org)
  • By combining gene function, ontology, pathways and statistical analysis tools, PANTHER enables biologists to analyze large-scale, genome-wide data obtained from the current advance technology including: sequencing, proteomics or gene expression experiments. (wikipedia.org)
  • alleles
  • The field also includes studies of intragenomic (within the genome) phenomena such as epistasis (effect of one gene on another), pleiotropy (one gene affecting more than one trait), heterosis (hybrid vigour), and other interactions between loci and alleles within the genome. (wikipedia.org)
  • ontologies
  • These ontologies and annotations will be accessible from our species' database web sites and from a jointly developed web site. (jax.org)
  • Consortium
  • We collaborate with phenotyping/mutagenesis/targeting programs such as the International Mouse Mutagenesis Consortium, the Complex Trait Consortium, the Phenome Project, the International Gene Trap Consortium, and the Knockout Mouse Project (KOMP). (jax.org)
  • We work with the IMAGE consortium to pre-assign MGI accession numbers to IMAGE clones, which are, in turn, sequenced by Washington University. (jax.org)
  • Marker
  • We provide links from our marker detail page to the Mouse GeneView of the Ensembl Genome Browser. (jax.org)
  • These EST resources provide the basis for future microarray development, marker validation, genetic linkage mapping and QTL analysis in Dioscorea species. (biomedcentral.com)
  • transcriptional
  • Our analysis suggests that apart from transcriptional regulation, post-transcriptional alternative splicing in some members of this family takes place during growth and development, in various tissues and during biotic and abiotic stresses. (springer.com)
  • functional
  • Bratić AM, Majić DB, Samardžć JT, Maksimović VR (2009) Functional analysis of the buckwheat metallothionein promoter: tissue specificity pattern and up-regulation under complex stress stimuli. (springer.com)
  • amino acid seq
  • Following Rosalind Franklin's confirmation of the helical structure of DNA, James D. Watson and Francis Crick's publication of the structure of DNA in 1953 and Fred Sanger's publication of the Amino acid sequence of insulin in 1955, nucleic acid sequencing became a major target of early molecular biologists. (wikipedia.org)
  • In addition to his seminal work on the amino acid sequence of insulin, Frederick Sanger and his colleagues played a key role in the development of DNA sequencing techniques that enabled the establishment of comprehensive genome sequencing projects. (wikipedia.org)
  • These were predicted using the NetNGlyc program from ExPASy and the TMEM63A amino acid sequence, as well as the inferred orientation of the protein in the membrane. (wikipedia.org)
  • freely available
  • UCSF Chimera is a versatile molecular visualization and analysis system that is freely available to the academic community, government, and public and has been cited in more than 7,700 published scientific papers. (ucsf.edu)
  • expression
  • We collaborate with the Edinburgh Mouse Atlas and Gene Expression Database project to develop and extend an anatomical dictionary of mouse development and to build the Mouse Gene Expression Information Resource that will combine the use of controlled vocabularies and image-based methods for the representation and analysis of expression patterns. (jax.org)
  • Quantitative gene expression analysis aims to define the gene expression patterns determining cell behavior. (blogspot.com)
  • We have studied the global gene expression profiles of normal and Ts65Dn male and normal female mice brains (P30) using the serial analysis of gene expression (SAGE) technique. (blogspot.com)
  • These observations have important implications for the design of future microarray-based studies in T1D and, more generally, for studies that aim to combine genome -wide expression profiling and congenic mapping. (blogspot.com)
  • Therefore, an improved method called serial analysis of gene expression (SAGE) is also used. (wikipedia.org)
  • This method identifies, for each cDNA transcript molecule produced from a cell's gene expression, regions only 10-14 bases long anywhere along the read sequence, sufficient to uniquely identify that cDNA transcript. (wikipedia.org)
  • BioGPS analysis for TMEM63A in humans shows that the gene is ubiquitously expressed, with the highest levels of expression found in T-cells and dendritic cells. (wikipedia.org)
  • Analysis of TMEM63A expression in the mouse using BioGPS revealed more variable expression patterns, with the highest expression being seen in the stomach and large intestine. (wikipedia.org)
  • obsolete
  • Lastly, we recognize that biomedical research is inheriently dynamic and although we do our best to keep these project descriptions up to date it is unavoidable that some become stale or obsolete. (ucsf.edu)
  • This sort of laborious effort can be rendered obsolete by genome-scale mapping projects. (genetics.org)
  • researchers
  • In this project we will develop new tools within Chimera that support analysis of quaternary levels of structure, serving researchers using the techniques of electron cryo-microscopy (cryoEM) single particle reconstruction and tomography, x-ray crystallography, and high-resolution three-dimensional light microscopy. (ucsf.edu)
  • Chimera has become the leading package for cryoEM researchers analyzing density maps and atomic models of large molecular assemblies. (ucsf.edu)
  • Research
  • Funding for is provided by the National Institutes of Health, the Wellcome Trust, GlaxoSmithKline, the Merck Genome Research Institute and Affymetrix Inc. Sequencing partners are the Sanger Institute, the Whitehead Institute for Biomedical Research and Washington University School of Medicine. (jax.org)
  • Genome Research, 22 , 1775. (springer.com)
  • Genome Research, 14 , 331. (springer.com)