http://precedings.nature.com/tags/genomics Recently posted documents tagged with 'genomics' Nature Publishing Group en Nature Precedings http://precedings.nature.com/images/header_logo.gif http://precedings.nature.com http://dx.doi.org/10.1038/npre.2009.3981.1 Sir Charles Snow, being a writer and a scientist, felt that he “was moving among two groups – comparable in intelligence, identical in race, not grossly different in social origin, earning about the same incomes, who had ceased to communicate at all”(Snow, 1993 [1959], p.2). He called these two groups, the two cultures, referring to those in the natural sciences and those in the humanities. Many argue that this division is an awful thing. This poster discusses strategies to reacquaint the two cultures in the case of genomics. http://dx.doi.org/10.1038/npre.2009.3981.1 Tue, 17 Nov 2009 11:28:40 UTC Reacquainting two cultures. Preventing a de-elsification of European nutrigenomics? doi:10.1038/npre.2009.3981.1 2009-11-17 Bart Penders Nature Precedings 2009-11-17T11:28:40Z Poster Genetics & Genomics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3900.1 Analyzing of sequences similarities is the first and most important method used to find out the function of unknown nucleotides. Searching of homologs should be done carefully not to loose any important ones. Having thousands of results from various long-read sequencing projects (ie. differentially expressed tags, genomic polymorphons or BAC ends), the by-hand ability to retrieve interesting (to our goal) similarities in hundreds of Blast results decreases rapidly. Decreasing the number of retrieved sequences by giving more stringency in e-value threshold or displaying less results could lead to false deductions. Functional genomics, proteomics and metabolomics could give us answers to the role of nucleotide sequences. It makes the need to annotate as much of the homologies as we can, to proper molecular function, biological process and cellular component (as its proposed by widely accepted Gene Ontology Consortium annotations or MapMan mappings by Max-Planc-Institute). To facilitate fast retrieval of interesting Blast homologies and making right deductions about the biological role of sequences, in big sequencing projects, the new Perl script BRAGOMAP was written. The program make use of some of BioPerl modules as well as the power of regex text-mining in the Perl itself. The script gives us the possibility to find interesting sequence similarities by using keywords and giving points for each one found. It collects all important information from the GenBank data and puts it in different columns of tab-delimited file for further use. If we were interested (for example) in flower differentiation genes we could use the keywords (flower, ovule, anther, etc.) and/or filter all the homologies isolated from flower tissues in a special development stage. We can also filter results by choosing similarities to interesting genes or protein products. This script retrieve also all standard information from the Blast and GenBank files as Description, ACC no., E-value, Similarity positions, Query Length, Percent of Similarity etc. Automatic GO and MapMan annotations are done by looking for genes, protein products and /or DB references in the proper mappings files. Here we present the usefulness of the script in analyzing sequence similarities and annotations mapping of 3855 BAC ends obtained from the HindIII BAC genomic library of cucumber (Cucumis sativus L., line B10). http://dx.doi.org/10.1038/npre.2009.3900.1 Mon, 26 Oct 2009 11:35:28 UTC BRAGOMAP – a new Perl script for high throughoutput blast results analysis including GO and MapMan automatic annotations doi:10.1038/npre.2009.3900.1 2009-10-26 Rafal Woycicki Nature Precedings 2009-10-26T11:35:28Z Poster Genetics & Genomics Bioinformatics Plant Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3167.1 So far researchers, web users were restricted to non-intuitive and visually poor text based databases every time they wanted to take a look on the mitochondrial DNA and find a region of interest. But with MitoWheel the situation is about to change. MitoWheel is a graphical representation of the circular human mitochondrial genome available on the web at http://mitowheel.org.The human mitochondrial DNA is a 16569 basepair long, circular molecule and this very circularity is the basic idea behind MitoWheel. The mitochondrial genome can be represented with a wheel and by spinning this wheel users can quickly scan through, browse and identify the particular regions. The spinning is via click-and-drag or by using the left and right arrows in the sequence bar.The sequence used is the standard Revised Cambridge Reference Sequence. The main components of the application are a search box, a sequence bar and the wheel itself.The most important feature of the MitoWheel is its versatile search function. As an output of a query the wheel and the sequence bar stops at the searched nucleotide position or sequence and additional information (whether the nucleotide or the sequence is part of a gene or other specific region) can be seen on a pop-up window. People can search for a nucleotide position or sequence in the search box with numbers (15450, 8366-8572), with nucleotides (ATGCTAAAA), search for an encoded gene or specific region by abbreviations (atp8), genes (complex III, cytochrome b) and sequence features, even mutations (12276A) with the possible functional effects of the mutation. Selected sequences or their reverse complementary sequences can be send to the clipboard and saved.MitoWheel incorporates data on fully sequenced human mitochondrial genomes that have been deposited in the GenBank nucleotide database by different research groups. The sequence bar contains information not only about the function of specific nucleotides, but also about allele frequencies at polymorphic positions.MitoWheel was developed by human mitochondrial geneticist Gábor Zsurka, the wheel was made with Flash Professional 8.0 and the code harnessed the power of Actionscript, a scripting language designed specially for Flash. Attila Csordás is the other member of the developer group. The web application can be useful for anybody interested in human mitochondrial genetics and its biological, medical consequences. http://dx.doi.org/10.1038/npre.2009.3167.1 Thu, 07 May 2009 15:03:08 UTC MitoWheel, visualizing the human mitochondrial genome doi:10.1038/npre.2009.3167.1 2009-05-07 Attila Csordás Nature Precedings 2009-05-07T15:03:08Z Poster Genetics & Genomics Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3180.1 With the objective of elucidating the structure of gene interactions in the human genome, the Genome Network Project has generated a vast quantity of experimental data, mainly focusing on transcriptional control and transcription-factor related protein-protein interactions (PPI). This data has been collected and organized into the Genome Network Platform (http://genomenetwork.nig.ac.jp/) at the National Institute of Genetics. Expression data was obtained through CAGE (Cap Analysis Gene Expression), qRT-PCR, tiling array, microarray and short RNA analysis, while PPI information was gathered through yeast two hybrid (Y2H), mammalian two hybrid (M2H) and in vitro virus (IVV) methods. The Genome Network Platform Viewer provides an integrated user interface to the complete database, including services of gene search, whole genome browsing, PPI network viewer, and expression profile analysis. Our platform represents an extremely useful resource for researchers in the field of genomics, and provides access to high quality data through the combination of intuitive browsing and visualization capabilities. http://dx.doi.org/10.1038/npre.2009.3180.1 Tue, 28 Apr 2009 18:25:42 UTC Genome Network Project: An Integrated Genomic Platform doi:10.1038/npre.2009.3180.1 2009-04-28 So Nakagawa Nature Precedings 2009-04-28T18:25:42Z Poster Genetics & Genomics Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3170.1 Although there is significant optimism that community involvement can drive genome curation, results to date are disappointing. The Human Genome and Saccharomyces Genome Databases both tried community annotation experiments and few community contributions were obtained. JCVI’s own early experiences with community curation were also largely unsuccessful. Although community curation tools were publicly available on JCVI web resources and much effort was made by JCVI personnel to advertise these resources, little curation was actually submitted. Starting in late 2007, JCVI’s model for community curation changed. Instead of simply providing curation tools on websites and advertising their utility at meetings and conferences, JCVI instituted a community curation jamboree model. Annotation jamborees are an excellent form of outreach to the community. JCVI’s experience conducting jamborees is highly successful, demonstrating that jamborees are effective tools for incorporating expert annotation data into existing genome submissions, updating existing annotation, tagging annotation with updated experimental references and providing the community with opportunities to become familiar with JCVI’s annotation procedures and curation tools. Jamborees provide a means to directly interact with the community and integrate their research expertise into genomic data sets. Jamboree participants are encouraged to provide their expert input by focusing on their genes and gene families of interest, particularly those with supporting experimental evidence. Through JCVI’s NIAID Bioinformatics Resource Center, Pathema (http://pathema.jcvi.org), JCVI hosted two annotation jamborees incorporating expert annotation into Entamoeba and Burkholderia genome projects. These jamborees resulted in curation of 1,565 functional assignments, 3,499 Gene Ontology terms, 129 gene structures, and 296 experimental references for 11 genome projects representative of the Pathema data set. Researchers who contributed to annotation at these jamborees are being submitted as contributing authors on annotation update submissions made to GenBank for those organisms. Additionally, the annotation associated with the submission is recognized as part of community curation efforts and collaboration, and all updates and contributions are reflected on the Pathema web resource.The networking and personal communication that occurs throughout a jamboree facilitates a forum for research and data exchange, solicitation of user feedback and the establishment of new community collaborations. Although integrating and updating annotation data is important, it is our experience that the interactions that occur and collaborations that are formed are the most beneficial long-term results of jamboree efforts. Collaborations we established as a direct result of jamboree activity include continued community annotation, custom data analyses and general informatics support not otherwise solicited by the researcher. For the jamborees JCVI recently hosted, we established successful collaborations with four researchers who continued to provide curation from their own institute. http://dx.doi.org/10.1038/npre.2009.3170.1 Fri, 24 Apr 2009 18:55:09 UTC Expert Assertions Through Community Annotation Jamborees doi:10.1038/npre.2009.3170.1 2009-04-24 Lauren Brinkac Nature Precedings 2009-04-24T18:55:09Z Presentation Genetics & Genomics Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2009.3134.1 The concept of community annotation is a growing discipline for achieving participation of the research community in depositing up‐to‐date knowledge in biological databases.The Solanaceae Genomics Network (SGN) is a clade‐oriented database (COD) focusing on plants of the nightshade family, including tomato, potato, pepper, eggplant, and tobacco, and is one of the bioinformatics nodes of the international tomato genome sequencing project. One of our major efforts is linking Solanaceae phenotype information with the underlying genes, and subsequently the genome. As part of this goal, SGN has introduced a database for locus names and descriptors, and a database for phenotypes of natural and induced variation. These two databases have web interfaces that allow cross references, associations with tomato gene models, and in‐house curated information of sequences, literature, ontologies, gene networks, and the Solanaceae biochemical pathways database (SolCyc). All of our curator tools are open for online community annotation, through specially assigned “submitter” accounts. Currently the community database consists of 5,548 phenotyped accessions, and 5,739 curated loci, out of which more than 300 loci where contributed or annotated by 66 active submitters, creating a database that is truly community driven.This framework is easily adaptable for other projects working on other taxa (for example see http://chlamybase.org), greatly expanding the application of this user‐friendly online annotation system. Community participation is fostered by an active outreach program that includes contacting potential submitters via emails, at meetings and conferences, and by promoting featured user submitted annotations on the SGN homepage. The source code and database schema for all SGN functionalities are freely available. Please contact SGN at sgn‐feedback[at]sgn.cornell.edu for more information. http://dx.doi.org/10.1038/npre.2009.3134.1 Wed, 22 Apr 2009 21:15:52 UTC The SOL Genomics Network Model: Making Community Annotation Work doi:10.1038/npre.2009.3134.1 2009-04-22 Naama Menda Nature Precedings 2009-04-22T21:15:52Z Poster Bioinformatics Plant Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2008.2221.1 The GABI Primary Database, GabiPD, was established eight years ago in the frame of the German initiative for Genome Analysis of the Plant Biological System (Genomanalyse im biologischen System Pflanze, GABI), funded by the German Federal Ministry of Education, Research and Technology (BMBF) as well as a number of private enterprise companies. The main goal of GabiPD is to collect, integrate, visualize and link primary information from GABI projects. GabiPD, in contrast to other plant databases constitutes a repository and analysis platform for a wide array of heterogeneous data arising from high-throughput experiments in several plant species. Currently, data from different ‘omics’ fronts are incorporated in GabiPD (i.e., genomics, transcriptomics, metabolomics, proteomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for text based retrieval of all data types in GabiPD (e.g., clones, genes, mutant plant lines, markers). All data types are pointing to the central Gene’s GreenCard, where gene information is integrated from genome annotation projects. Within the Gene’s GreenCards links to all GabiPD data related to the corresponding genes as well as cross references to large UniGene sets from NCBI and to useful gene-based external data bases are displayed. A collection of ~400000 ESTs from different species, generated in different GABI projects, is made publicly available though GabiPD. These ESTs have been cross referenced to UniGene sets from NCBI and to sequences from different plant genome projects, in an effort to ease the transfer of functional information. The centralized Gene’s GreenCard also allows visualizing ESTs aligned to annotated transcripts as well as identified protein domains and gene structure. Moreover GabiPD makes available interactive genetic maps from Solanum tuberosum (potato) and Hordeum vulgare (barley). Gene expression data in GabiPD can be visualized through MapManWeb, the web interface of MapMan. Access to the data in GabiPD is provided via either the web interface (http://www.gabipd.org) or webservices that are currently available for Arabidopsis-related information. GabiPD was accessed by more than 30000 unique visitors last year from around the world. http://dx.doi.org/10.1038/npre.2008.2221.1 Fri, 22 Aug 2008 20:56:52 UTC GabiPD: GABI primary database – a plant integrative ‘omics’ database doi:10.1038/npre.2008.2221.1 2008-12-04 Diego Mauricio Riaño-Pachón Nature Precedings 2008-08-22T20:56:52Z Poster Bioinformatics Plant Biology http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2008.2210.1 The GABI Primary Database, GabiPD (http://www.gabipd.org/), was established in the frame of the German initiative for Genome Analysis of the Plant Biological System (GABI). The goal of GabiPD is to collect, integrate, analyse and visualise primary information from GABI projects. GabiPD constitutes a repository and analysis platform for a wide array of heterogeneous data from high-throughput experiments in several plant species. Data from different ‘omics’ fronts are incorporated (i.e., genomics, transcriptomics, proteomics and metabolomics), originating from 14 different model or crop species. We have developed the concept of GreenCards for text based retrieval of all data types in GabiPD (e.g., clones, genes, mutant lines). All data types point to a central Gene GreenCard, where gene information is integrated from genome projects or NCBI UniGene sets. The centralised Gene GreenCard allows visualising ESTs aligned to annotated transcripts as well as displaying identified protein domains and gene structure. Moreover GabiPD makes available interactive genetic maps from potato and barley, and 2DE-gels from Arabidopsis thaliana and Brassica napus. Gene expression and metabolic profiling data can be visualised through MapManWeb. By the integration of complex data in a framework of existing knowledge, GabiPD provides new insights and allows for new interpretations of the data. http://dx.doi.org/10.1038/npre.2008.2210.1 Fri, 22 Aug 2008 09:31:55 UTC GabiPD: The GABI Primary Database – a plant integrative ‘omics’ database doi:10.1038/npre.2008.2210.1 2008-08-22 Diego Mauricio Riaño-Pachón Nature Precedings 2008-08-22T09:31:55Z Manuscript Genetics & Genomics Molecular Cell Biology Bioinformatics http://creativecommons.org/licenses/by/3.0/ http://dx.doi.org/10.1038/npre.2008.1684.1 GabiPD (http://gabi.rzpd.de) was established within GABI-I and further developed in GABI-II and constitutes a repository and analysis platform for a wide array of heterogeneous data arising from high throughput experiments developed by members of the GABI/WPG community. Currently, data from different fronts (genomics, transcriptomics, proteomics, metabolomics) are incorporated in GabiPD, representing 14 different biological species. Last year GabiPD moved to the Max Planck Institute of Molecular Plant Physiology. In the progressing GABI-FUTURE phase, the GabiPD team has been creating a more integrative data view, expanding the tools and information provided by our well-known GreenCards. Links to different species-specific (Arabidopsis thaliana so far) GABI-resources (e.g., Aramemnon, GABI-KAT) as well as external resources (e.g., ProMEX) are being added or updated. All data types (e.g., protein spots, clones) in GabiPD are pointing to the central Gene’s GreenCard, where gene information is retrieved from genome annotation projects or large UniGene sets provided by NCBI. Moreover, the GabiPD team will perform new types of data computations, like analysis of conserved domains in protein sequences. http://dx.doi.org/10.1038/npre.2008.1684.1 Thu, 13 Mar 2008 12:46:38 UTC GabiPD: Gabi Primary Database – a plant integrative ‘omics’ database in GABI-FUTURE doi:10.1038/npre.2008.1684.1 2008-12-04 Diego Mauricio Riaño-Pachón Nature Precedings 2008-03-13T12:46:38Z Poster Bioinformatics Plant Biology http://creativecommons.org/licenses/by/3.0/