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http://the_brain.bwh.harvard.edu/uniprobe/

Database that hosts experimental data from universal protein binding microarray (PBM) experiments (Berger et al., 2006) and their accompanying statistical analyses from prokaryotic and eukaryotic organisms, malarial parasites, yeast, worms, mouse, and human. It provides a centralized resource for accessing comprehensive data on the preferences of proteins for all possible sequence variants ("words") of length k ("k-mers"), as well as position weight matrix (PWM) and graphical sequence logo representations of the k-mer data. The database's web tools include a text-based search, a function for assessing motif similarity between user-entered data and database PWMs, and a function for locating putative binding sites along user-entered nucleotide sequences.

Proper citation: UniPROBE (RRID:SCR_005803) Copy   

•   Source: SciCrunch Registry

http://edwardslab.bmcb.georgetown.edu/downloads/

The Peptide Sequence Database contains putative peptide sequences from human, mouse, rat, and zebrafish. Compressed to eliminate redundancy, these are about 40 fold smaller than a brute force enumeration. Current and old releases are available for download. Each species'' peptide sequence database comprises peptide sequence data from releveant species specific UniGene and IPI clusters, plus all sequences from their consituent EST, mRNA and protein sequence databases, namely RefSeq proteins and mRNAs, UniProt''s SwissProt and TrEMBL, GenBank mRNA, ESTs, and high-throughput cDNAs, HInv-DB, VEGA, EMBL, IPI protein sequences, plus the enumeration of all combinations of UniProt sequence variants, Met loss PTM, and signal peptide cleavages. The README file contains some information about the non amino-acid symbols O (digest site corresponding to a protein N- or C-terminus) and J (no digest sequence join) used in these peptide sequence databases and information about how to configure various search engines to use them. Some search engines handle (very) long sequences badly and in some cases must be patched to use these peptide sequence databases. All search engines supported by the PepArML meta-search engine can (or can be patched to) successfully search these peptide sequence databases.

Proper citation: Peptide Sequence Database (RRID:SCR_005764) Copy   

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http://h-invitational.jp/varygene/

It consists of a Genome Browser, an LD Search System, and the VaryGene 2 system. The Generic Genome Browser is a combination of database and interactive Web page for manipulating and displaying annotations on genomes, while LDSearchSystem is a search system for linkage disequilibrium (LD) bins. VaryGene 2 is a system to search, display, and download our research results on human polymorphism based on publicly available data and annotations of transcripts presented by H-InvDB. VaryGene 2 provides information about single nucleotide polymorphisms (SNPs), deletion-insertion polymorphisms (DIPs), short tandem repeats (STRs), single amino acid repeats (SARs), structural variation (or copy number variations: CNVs), and their relations to the genome, transcripts, and functional domains. Users can search by polymorphisms, transcripts, STRs/SARs, and CNVs.

Proper citation: VarySysDB (RRID:SCR_005880) Copy   

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http://indel.bioinfo.sdu.edu.cn/gridsphere/gridsphere

THIS RESOURCE IS NO LONGER IN SERVCE, documented September 2, 2016. Indel Flanking Region Database is an online resource for indels and the flanking regions of proteins in SCOP superfamilies, including amino acid sequences, lengths, locations, secondary structure constitutions, hydrophilicity / hydrophobicity, domain information, 3D structures and so on. It aims at providing a comprehensive dataset for analyzing the qualities of amino acid insertion/deletions(indels), substitutions and the relationship between them. The indels were obtained through the pairwise alignment of homologous structures in SCOP superfamilies. The IndelFR database contains 2,925,017 indels with flanking regions extracted from 373,402 structural alignment pairs of 12,573 non-redundant domains from 1053 superfamilies. IndelFR has already been used for molecular evolution studies and may help to promote future functional studies of indels and their flanking regions.

Proper citation: IndelFR - Indel Flanking Region Database (RRID:SCR_006050) Copy   

•   Source: SciCrunch Registry

http://www.utrome.org

This database is intended as a comprehensive resource for UTR (Untranslated Region) biology in C. elegans. The database provides detailed information on UTR structures for all protein-coding mRNAs, and includes annotations extracted from other databases (such as WormBase and PicTar) as well as new annotations generated as part of the NYU UTRome project (including preliminary characterization of UTR clones, USTs (UTR sequence tags), curated sequences, and computational and experimental analysis of functional elements). Examples of functional elements within UTRs include predicted and validated microRNA (miRNA) binding sites (responsible for post-transcriptional gene regulation), putative consensus signals for polyA addition, and predicted secondary structures (which may influence the biological activity of UTRs). The UTRome project is part of the ModEncode Consortium, an NIH initiative to characterize at a genomic scale functional sequence elements encoded in the worm (C. elegans) and fly (D. melanogaster) genomes. UTRs are important portions of mRNAs required for post-transcriptional regulation by interacting with proteins or non-coding RNAs (e.g. microRNAs). To study the role of UTRs we are building a UTR database for C. elegans.

Proper citation: UTRome.org (RRID:SCR_005878) Copy   

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http://roar.eprints.org/

Listing of institutional repositories for depositing preprints of published materials with the aim of promoting the development of open access by providing timely information about the growth and status of repositories throughout the world. Open access to research maximizes research access and thereby also research impact, making research more productive and effective. Repository Types: * Research Institutional or Departmental * Research Multi-institution Repository * Research Cross-Institutional * e-Journal/Publication * e-Theses * Database/A&I Index * Research Data * Open and Linked Data * Learning and Teaching Objects * Demonstration * Web Observatory * Other Repository Software: * ARNO * Bepress * CDS Invenio * ContentDM by OCLC * DIGIBIB * DigiTool * DiVA * DoKS * DSpace * EDOC * EPrints * Equella * ETD-db * Fedora ** Fez * Greenstone * HAL * i-Tor * IntraLibrary * Keystone DLS * MiTOS * MyCoRe * Open Journal System * Open Repository * OPUS (Open Publications System) * Other softwares (various) * PMB Services * SBCAT * SciX * SobekCM * WIKINDX * Zentity

Proper citation: ROAR (RRID:SCR_005951) Copy   

•   Source: SciCrunch Registry

http://www.youtube.com/user/NIGMS/

YouTube videos provided by the National Institute of General Medical Sciences (NIGMS).

Proper citation: NIGMS - YouTube (RRID:SCR_005678) Copy   

•   Source: SciCrunch Registry

http://tolweb.org/tree/

A collection of information about biodiversity compiled collaboratively by hundreds of expert and amateur contributors. Its goal is to contain a page with pictures, text, and other information for every species and for each group of organisms, living or extinct. Connections between Tree of Life web pages follow phylogenetic branching patterns between groups of organisms, so visitors can browse the hierarchy of life and learn about phylogeny and evolution as well as the characteristics of individual groups.

Proper citation: Tree of Life Web Project (RRID:SCR_005673) Copy   

•   Source: SciCrunch Registry

http://gopubmed.org/web/gopubmed/

A web server which allows users to explore PubMed search results with the Gene Ontology, a hierarchically structured vocabulary for molecular biology. GoPubMed submits a user''''s keywords to PubMed, retrieves the abstracts, detects Gene Ontology terms in the abstracts, displays the subset of Gene Ontology relevant to the original query, and allows the user to browse through the ontology displaying associated papers and their GO annotation. Platform: Online tool

Proper citation: GoPubMed (RRID:SCR_005823) Copy   

•   Source: SciCrunch Registry

http://nmr.cmbi.ru.nl/NRG-CING/HTML/index.html

NRG-CING presents a complete validation report for all 9,000+ wwPDB NMR entries including remediated experimental data such as chemical shifts from BMRB and restraints from NRG . These CING reports are compiled from internal analyses and those by CCPN, DSSP, PROCHECK-NMR/Aqua, ShiftX, Talos+, Vasco, Wattos, and WHAT_CHECK. The NRG-CING website is a collection of CING reports that has been pre-calculated for all PDB files solved by NMR. (See website for more information on CING.) In case the underlying experimental data is available, these have been cleaned up and made syntactically and semantically correct and homogeneous. For many macromolecular NMR ensembles from the Protein Data Bank (PDB) the experiment-based restraint lists used in the structure calculation are accessible, while other experimental data, mainly chemical shift values, are often available from the BioMagResBank. Assessment of the quality of the structural result is paramount to their usage and a combined, integrated repository of both input data and structural results greatly facilitates such an analysis. In addition, the accuracy and precision of the coordinates in these macromolecular NMR ensembles can be improved by recalculations using the available experimental data and present-day software with improved protocols and force fields. Such efforts, however, generally fail on over half of all deposited structures due to the syntactic and semantic heterogeneity of the data and the wide variety of formats used for their deposition. We have combined the cleaned-up restraints information from the NMR Restraints Grid (NRG) database with available chemical shifts from the BioMagResBank in the weekly updated NRG-CING database. Eleven programs, in addition to CING itself, have been included in the NRG-CING production pipeline to arrive at validation reports that list for each entry the potential inconsistencies between the coordinates and the available restraint and chemical shift data. The longitudinal validation of this data yielded a set of indicators that can be used to judge the quality of every macromolecular structure solved with NMR. The cleaned up NMR experimental datasets and the validation reports are freely available.

Proper citation: NRG-CING (RRID:SCR_006079) Copy   

•   Source: SciCrunch Registry

http://yh.genomics.org.cn

This database presents the entire DNA sequence of the first diploid genome sequence of a Han Chinese, a representative of Asian population. The genome, named as YH, represents the start of YanHuang Project, which aims to sequence 100 Chinese individuals in 3 years. It was assembled based on 3.3 billion reads (117.7Gbp raw data) generated by Illumina Genome Analyzer. In total of 102.9Gbp nucleotides were mapped onto the NCBI human reference genome (Build 36) by self-developed software SOAP (Short Oligonucleotide Alignment Program), and 3.07 million SNPs were identified. The personal genome data is illustrated in a MapView, which is powered by GBrowse. A new module was developed to browse large-scale short reads alignment. This module enabled users track detailed divergences between consensus and sequencing reads. In total of 53,643 HGMD recorders were used to screen YH SNPs to retrieve phenotype related information, to superficially explain the donor's genome. Blast service to align query sequences against YH genome consensus was also provided.

Proper citation: YanHuang Project (RRID:SCR_006077) Copy   

•   Source: SciCrunch Registry

http://trbase.ex.ac.uk/

This TRbase is a relational tandem repeat database that relates tandem repeats to gene locations and disease genes of the human genome. The TRbase stores both perfect and imperfect repeats of 1 to 2000 bp unit lengths that were identified using the Tandem Repeat Finder program. Disease information for all 24 chromosomes was retrieved from the Online Mendelian Inheritance in Man (OMIM) database. There are five main search forms by which the user may query the database: 1. The Advanced tandem repeat search: This allows a complete search for tandem repeats using a combination of criteria, such as total tandem repeat length, repeat unit length, copy number of the repeats, percentage matches and the consensus repeat pattern. On submission, the number of repeats and the detailed tandem repeat characteristics of each repeat that match the user query are tabulated. 2. The Main search: This relates tandem repeat data to genes and diseases. The user may specify a gene of interest to view details of all repeats associated with it or search for tandem repeats present in a particular disease by entering the name/keyword for the disease or the MIM number of the disease gene. 3. The Composite search: This more advanced search allows the user to query specifically for repeats present in exons, introns or intergenic regions of a gene or disease gene. 4. The Gene Search: Further information on genes can be available by a simple gene name search on this page. 5. The Disease search: This allows extensive information on disease genes on all chromosomes of the human genome. Searching for a MIM number, or keyword searches specifying the features of the disease, will retrieve the information on the disease and the chromosome in which the disease gene occurs. Each entry retrieved is linked to the OMIM database for detailed literature and gene map information on the disease.

Proper citation: TRbase: A Database Of Tandem Repeats In The Human Genome (RRID:SCR_005658) Copy   

•   Source: SciCrunch Registry

http://possum.cbrc.jp/PoSSuM/

Relational database of all the discovered similar pairs in a huge number of protein-ligand binding sites with annotations of various types (e.g., CATH, SCOP, EC number, Gene ontology). They used a tremendously fast algorithm called SketchSort that enables the enumeration of similar pairs in a huge number of protein-ligand binding sites. They conducted all-pair similarity searches for 3.4 million known and potential binding sites using the proposed method and discovered over 24 million similar pairs of binding sites. PoSSuM enables rapid exploration of similar binding sites among structures with different global folds as well as similar ones. Moreover, PoSSuM is useful for predicting the binding ligand for unbound structures. Basically, the users can search similar binding pockets using two search modes: # Search K is useful for finding similar binding sites for a known ligand-binding site. Post a known ligand-binding site (a pair of PDB ID and HET code) in the PDB, and PoSSuM will search similar sites for the query site. # Search P is useful for predicting ligands that potentially bind to a structure of interest. Post a known protein structure (PDB ID) in the PDB, and PoSSuM will search similar known-ligand binding sites for the query structure.

Proper citation: PoSSuM (RRID:SCR_006109) Copy   

•   Source: SciCrunch Registry

http://tandem.bu.edu/cgi-bin/trdb/trdb.exe

A public repository of information on tandem repeats in genomic DNA and contains a variety of tools for their analysis. These currently include the Tandem Repeats Finder algorithm, query and filtering capabilities for finding particular repeats of interest, repeat clustering algorithms based on sequence similarity, polymorphism prediction based on common patterns of mutation, PCR primer selection, and data download in a variety of formats. In addition, TRDB serves as a centralized research workbench, provides storage space for results of analysis, and permits collaborators to privately share their data and analysis.

Proper citation: Tandem Repeats Database (RRID:SCR_005659) Copy   

•   Source: SciCrunch Registry

http://opencitations.net/

Database of biomedical literature citations, harvested from the reference lists of all open access articles in PubMed Central that reference ~20% of all PubMed Central papers (approx. 3.4 million papers), including all the highly cited papers in every biomedical field. All the data are freely available for download and reuse. The web site allows these bibliographic records and citations to be browsed, individual articles to be selected, and its citation network to be visualized in a variety of displays. Details of each selected reference, and the data and diagrams for its citation network, may be downloaded in a variety of formats, while the entire Open Citations Corpus can be downloaded from our source data page in several formats including RDF and BibJSON. Their aim for the future is to work with publishers to make available the reference lists from many more current and recent journal articles, starting with the biomedical literature, and to make the citations contained within them available as Open Linked Data in the manner demonstrated by the existing exemplar data available here.

Proper citation: JISC Open Citations (RRID:SCR_005936) Copy   

•   Source: SciCrunch Registry

http://worfdb.dfci.harvard.edu/

Database that integrates and disseminates the data from the cloning of complete set of predicted protein-encoding ORFs of Caenorhabditis elegans. It also allows the community to search for availability and quality of cloned ORFs. So far, ORF sequence tags (OSTs) obtained for all individual clones have allowed exon structure corrections for ORFs originally predicted by the C. elegans sequencing consortium. The database contains this OST information along with data pertinent to the cloning process.

Proper citation: WorfDB (RRID:SCR_006028) Copy   

•   Source: SciCrunch Registry

http://www.bionet.nsc.ru/trrd/

TRRD is a unique information resource, accumulating information on structural and functional organization of transcription regulatory regions of eukaryotic genes. Only experimentally confirmed information is included into TRRD. Transcription Regulatory Regions Database (TRRD) is developed for accumulation of experimental information on the structure-function features of regulatory regions of eukaryotic genes. Each entry of TRRD corresponds to a particular gene. The annotated part of an entry includes the structure-function description of gene regulatory regions composed by regulatory units (promoters, silencers, enhancers, etc.), individual transcription factor binding sites that constitute these regulatory units, and transcription factors that bind to these sites. In addition, the entry contains the gene expression patterns and references to original publications.

Proper citation: Transcription Regulatory Regions Database (RRID:SCR_005723) Copy   

•   Source: SciCrunch Registry

http://202.120.189.88/drvis/

Dr.VIS collects and locates human disease-related viral integration sites. So far, about 600 sites covering 5 virus organisms and 11 human diseases are available. Integration sites in Dr.VIS are located against chromosome, cytoband, gene and refseq position as specific as possible. Viral-cellular junction sequences are extracted from papers and nucleotide databases, and linked to corresponding integration sites Graphic views summarizing distribution of viral integration sites are generated according to chromosome maps. Dr.VIS is built with a hope to facilitate research of human diseases and viruses. Dr.VIS provides curated knowledge of integration sites from chromosome region narrow to genomic position, as well as junction sequences if available. Dr.VIS is an open resource for free.

Proper citation: Dr.VIS - Human Disease-Related Viral Integration Sites (RRID:SCR_005965) Copy   

•   Source: SciCrunch Registry

http://www.ebi.ac.uk/thornton-srv/databases/FunTree/

FunTree provides a range of data resources to detect the evolution of enzyme function within distant structurally related clusters within domain super families as determined by CATH. To access the resource enter a specific CATH superfamily code or search for a structure / sequence / function (either via a EC code or KEGG ligand / reaction ID, PDB ID or UniProtKB ID). Or browse the resource via superfamily / function / structure / metabolites & reactions via the menu on the left panel. FunTree is a new resource that brings together sequence, structure, phylogenetic, chemical and mechanistic information for structurally defined enzyme superfamilies. Gathering together this range of data into a single resource allows the investigation of how novel enzyme functions have evolved within a structurally defined superfamily as well as providing a means to analyse trends across many superfamilies. This is done not only within the context of an enzyme''''s sequence and structure but also the relationships of their reactions. Developed in tandem with the CATH database, it currently comprises 276 superfamilies covering 1800 (70%) of sequence assigned enzyme reactions. Central to the resource are phylogenetic trees generated from structurally informed multiple sequence alignments using both domain structural alignments supplemented with domain sequences and whole sequence alignments based on commonality of multi-domain architectures. These trees are decorated with functional annotations such as metabolite similarity as well as annotations from manually curated resources such the catalytic site atlas and MACiE for enzyme mechanisms.

Proper citation: FunTree (RRID:SCR_006014) Copy   

•   Source: SciCrunch Registry

http://www.proquest.com/en-US/

Service that helps users navigate the research journey, connecting people and information from dissertations to governmental and cultural archives to news, in all its forms. Its role is essential to libraries and other organizations whose missions depend on the delivery of complete, trustworthy information. ProQuest''s massive information pool, built through partnerships with content creators, is navigated through technological innovations that enable users to quickly find just the right information. The ProQuest platform moves beyond navigation to empower researchers to use, create, and share contentaccelerating research productivity. The Summon web-scale discovery service is a boon to academic libraries worldwide. ProQuest expanded into corporate and government markets, with the ProQuest Dialog service and acquiring Congressional Information Services and University Publications of America. It acquired ebrary, expanding ProQuest''s content base to include e-books and adding to the technology expertise resident across the enterprise, which also includes such units as Serials Solutions, RefWorks-COS, and Bowker.

Proper citation: ProQuest (RRID:SCR_006093) Copy   

•   Source: SciCrunch Registry