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Showing 1 to 19 of 19 items tagged as sequencing


Structure (NCBI)

database

Provider: National Center for Biotechnology Information (NCBI)
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Descriptions: The NCBI Structure Group, a part of the Computational Biology Branch of NCBI, developed this suite of four free molecular and protein databases, each of which is itself made up of several others, and all of which can be searched individually. Macromolecular Structures, Conserved Domains, Small Molecules, and Biological Systems are the four main resources here- tools designed to facilitate discovery of sequence, function and structure associations. The tab labeled "Discover" does a good job of explaining how to use the Structure databases and how to access various facets of information on a molecule or protein from any point in NCBI's many resources.
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Structural Biology Knowledgebase

database

Provider: Nature.com and PSI (Protein Structure Initiative)
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Descriptions: The Structural Biology Knowledgebase (SBKB) is the product of a collaboration between the Protein Structure Initiative (PSI) and Nature Publishing Group (NPG.) The site offers an easy way of keeping up to date on the latest developments from the PSI, and more generally, in the fields of structural genomics and structural biology. Some areas of this site require a free registration involving affirmation of a statement declaring that one's purpose is strictly non-commercial and that one is an academic.
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UniProt

database

Provider: UniProt Consortium
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Descriptions: "The mission of UniProt is to provide the scientific community with a comprehensive, high-quality and freely accessible resource of protein sequence and functional information."  Available material consists of: UniProtKB, a two-section protein knowledge-base consisting of SwissProt and TrEMBL; UniRef (sequence clusters;) UniParc (a sequence archive for tracking sequences and identifiers) and the supporting data (literature citations, taxonomy, keywords, nomenclature, guidelines and indexes.) A user manual and primer on annotation are provided as well. UniProt is distributed free under a Creative Commons attribution license. Updates are frequent and updated releases must be downloaded from the website. Much of UniProt's funding is provided by the NIH.
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National Library of Medicine: Databases, Resources and APIs

database

Provider: National Library of Medicine
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Descriptions: This is NLM's portal to its approximately 300 research resources, from genetics to the history of medicine, from datasets to mobile apps.  Browse the list with all descriptive information, or search by subject term, type of data or tool, or by terms related to the content or intended audience.
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Proteopedia: Life in 3-D

database

Provider: Weizmann Institute of Science
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Descriptions: Proteopedia is a free, collaborative (wiki) 3-D encyclopedia of proteins and other molecules. The images can be reduced and restored by component with a toggle, or caused to rotate from any starting angle. Contains an introduction to structural biology and features sections on biomolecules, enzymes, metabolism, gene expression/replication, diseases, immune system, and methods of determining and analyzing structure and sequence. Contains a table of contents and a detailed structure index
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NextBio Basic

database

Provider: NextBio
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Descriptions: NextBio Basic is a free web application for searching biomedical and genetic information. It provides access to a 'curated, correlated database' of public data into which NextBio integrates Medline literature, clinical trial information, and news. Its semantic framework is based on gene, tissue, disease and compound ontologies. Registered users (registration for this basic version is free) can personalize their experience, communicate, collaborate and share data with the rest of the NextBio community. For the registered user, a single search for a gene yields quick results arranged by category: an overview of the gene; a list of tissues in which the gene is expressed; diseases and compounds relating to the gene; a list of the top associated researchers and authors; literature, associated clinical trials, and more.
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NDB: Nucleic Acid Database

database

Provider: The Nucleic Acids Database Research Project/Rutgers University
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Descriptions: A portal for 3-D structural information about nucleic acids, the NDB contains information about experimentally-determined nucleic acids and complex assemblies. Search by annotations relating to sequence, structure and function; download, analyze, and learn about nucleic acids.
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NCBI (National Center for Biotechnology Information)

database

Provider: National Center for Biotechnology Information/National Library of Medicine
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Descriptions: The National Center for Biotechnology Information advances science and health by providing access to biomedical and genomic information. NCBI provides a large number of resources for scientific research, including software and many databases.
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NBIC (Netherlands BioInformatics Centre)

website

Provider: Netherlands BioInformatics Centre
Descriptions: NBIC is engaged in bioinformatics research and education. Its website includes free software downloads, information on databases and projects, a journal and newsletter, and secondary-level education materials.
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GigaDB

database

Provider: GigaScience and BGI
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Descriptions: GigaDB is an open repository of datasets that support the research published in the open access BioMed Central bioinformatics journal, GigaScience. GigaDB provides a place from which to download supporting data and tools associated with papers published in GigaScience, thus facilitating the reproducibility of research. DataCite DOIs are assigned to these accompanying datasets, an identification device which serves to facilitate tracking and discoverability, and to provide additional credit to the authors who make their data publicly available.
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Interactive Fly

database

Provider: Society for Developmental Biology
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Descriptions: "A cyberspace guide to Drosophila development and metazoan evolution." This database won a Scientific American Sci-Tech Web Award (2002) and has also been featured in the Internet Scout Report. Sections: Biochemical Pathways, Organs, cis-Decoder, Labs and References, and more. Includes a gene index with extensive information on each gene, and a section on tissue and organ development.
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FlyBase: A Database of Drosophila Genes and Genomes

database

Provider: National Institutes of Health
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Descriptions: A visually beautiful, rich and well-organized home for Drosophila researchers, with forums, tools, links to other important sites (including Interactive Fly), high-quality images, a genome browser, and many more helpful tools and features. New FlyBase users can check under the News and link out to the explanatory article, FlyBase 101: the Basics of Navigating FlyBase. The FlyBase project is carried out by a consortium of Drosophila researchers and computer scientists from Harvard University, University of Cambridge, Indiana University and the University of New Mexico, and is funded by grants from NIH, British Medical Research Council, National Science Foundation, and Indiana University
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GQuery: Global Cross-database NCBI Search

database

Provider: National Center for Bioinformatics Information (NCBI)
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Descriptions: Integrated, text-based search and retrieval system used at the National Center for Biotechnology Information for its major databases: PubMed, Nucleotide and Protein Sequences, Protein Structures, Complete Genomes, Taxonomy, and others. GQuery integrates the scientific literature, DNA and protein sequence databases, 3D protein structure and protein domain data, population study datasets, expression data, assemblies of complete genomes, and taxonomic information into a tightly interlinked system.
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DBGET search

database

Provider: Kyoto University Bioinformatics Center
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Descriptions: DBGET is an integrated database retrieval system for accessing a web of molecular biology databases within GenomeNet and KEGG (Kyoto Encyclopedia of Genes and Genomes.)
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Center for Biological Sequence Analysis

database

Provider: Technical University of Denmark
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Descriptions: The Center does basic research in the fields of bioinformatics and systems biology. A multidisciplinary group of scientists works in ten specialist research areas (see the CBS Map) and is one of the largest such groups in European academia. Datasets, software, a publications list, and hundreds of links to other related data repositories are included here. Also includes a set of links to courses and lectures.
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BLAST (NCBI)

database

Provider: National Center for Biotechnology Information
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Descriptions: The Basic Local Alignment Search Tool (BLAST) finds regions of local similarity between sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance of matches. BLAST can be used to infer functional and evolutionary relationships between sequences as well as help identify members of gene families.
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BioMart Bio Portal

database

Provider: BioMart
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Descriptions: The BioMart project provides free software and data services to the international scientific community in order to foster scientific collaboration and facilitate the scientific discovery process. The project adheres to the open source philosophy of promoting collaboration and code reuse. The majority of the contributed databases are of plant or human genomics-oriented data. Under Community, view the linked database list with descriptions and contributor names. Databases originate from the UK, USA, France, Spain, China and other countries. There are three separate portal websites-- the central "Bio" portal, a cancer portal, and one for mouse data.  Unfortunately, no link back to BioMart is provided once the user accesses one of the other portals.
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DrugBank: Open Data Drug & Drug Target Database

database

Provider: David Wishart/University of Alberta, CA
Contents: ,
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Descriptions: A bio- and chemical informatics resource that combines detailed drug (chemical, pharmacological and pharmaceutical) data with comprehensive drug targeting (sequence, structure, and pathway) information. The database contains nearly 4300 drug entries, including FDA-approved small molecule drugs, FDA-approved biotech (protein/peptide) drugs, "nutraceuticals" and experimental drugs. Contains more than 6,800 drug entries with almost 4,300 non-redundant protein sequences linked. Each entry, or  DrugCard, contains more than 80 data fields, half of which are devoted to drug/chemical data and the other half to drug target/protein data. Downloads and information on rights, acknowledgement and usage are available here.
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1000 Genomes

database

Provider: 1000 Genomes
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Access Level:
Descriptions: 1000 Genomes: a deep catalog of human genetic variation "...is the first project to sequence the genomes of a large number of people, to provide a comprehensive resource on human genetic variation... The goal of the 1000 Genomes Project is to find most genetic variants that have frequencies of at least 1% in the populations studied." 1000 Genomes is an international endeavor, with participants from institutes, governments and universities world-wide. "DNA from the samples will be available for researchers to follow up with more detailed studies of variation in particular regions. The cell lines will allow researches to study cellular phenotypes such as gene expression, epigenetic patterns, and drug response. The extensive genotype data available on the samples, and the trio samples for some of the populations, will allow researchers to map regions of the genome computationally that affect the cellular phenotypes, and to study the heritability of these phenotypes."
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