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http://www.francisella.org/

Francisella tularensis is a Gram-negative bacteria that causes the disease tularemia. The genus also includes the strains Francisella novicida and Francisella holarctica, both of which are important research organisms. The biology, genomes and virulence capabilities of these organism are under active investigation in research institutions throughout the world. Our goal for the francisella.org website is to foster communication and collaboration among the Francisella tularensis research community. rancisella tularensis is a Gram-negative bacteria that causes the disease tularemia. The genus also includes the strains Francisella novicida and Francisella holarctica, both of which are important research organisms. The biology, genomes and virulence capabilities of these organism are under active investigation in research institutions throughout the world. Our goal for the francisella.org website is to foster communication and collaboration among the Francisella tularensis research community. Please visit the following sections of the website for more details about the tools currently available and those to be available in the near future. News 04/17/2008 F. novicida transposon mutant orders are now being handled by BEI Resources. 03/25/2008 New features have been added to the PSAT synteny analysis tool including a printer friendly version of the genomic neighborhood graphic, a text output of homologs in a region in spreadsheet format, and an option for displaying multiple alignments for a gene against a single comparison genome. 02/07/2008 Proteomics experimental data for F. novicida are now integrated into our genome browser. 02/05/2008 Updated genome annotations can now be submitted using the Panda tool. Your participation is encouraged. Please see the Panda page for more information. 02/04/2008 F. holarctica FTA is now available from Genbank (NC_009749) and has been added to our genome browser Tools Name Description Get surrounding sequence Given a gene, other genome feature, or genome coordinate, displays in FASTA format the surrounding sequence a specified number of nucleotides upstream and downstream Synteny Tool Analyze potential regions of local synteny between the Francisella genomes and any other published bacterial genome

Proper citation: Francisella tularensis Genome Research (RRID:SCR_013313) Copy   

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http://esharkgenome.imcb.a-star.edu.sg

To explore the elephant shark genome, we have conducted a survey-sequencing and comparative analysis of the elephant shark genome in collaboration with J. Craig Venter Institute. The elephant shark sequences generated under this project have been deposited at GenBank under the project accession number AAVX01000000. The sequences can also be searched using BLAST and retrieved here. Cartilaginous fishes (Chondrichthyes) represented by sharks, rays, skates and chimaeras, are phylogenetically the oldest group of living jawed vertebrates. They constitute an important group for our understanding of the origins of the complex developmental and physiological systems of jawed vertebrates. They are also an useful outgroup for bony vertebrates such as tetrapods and teleost fishes and help in identifying specialized features that have led to the evolution of diverse groups of bony vertebrates. The elephant shark (Callorhinchus milii), also known as the elephant fish and ghost shark, is a chimaera belonging to the Order Chimaeriformes and Family Callorhynchidae. It has the smallest genome among the known cartilaginous fish genomes. Thus, it was proposed as a model cartilaginous fish genome for whole-genome sequencing and comparative analysis (Venkatesh et al. 2005. Curr. Biol. 15: R82-R83). The following resources of the elephant shark are available for the scientific community: *Elephant Shark 1.4x assembly fasta sequences zipped 227 megabytes *Genomic DNA *~8x coverage BAC library (average insert size, ~150 kb) *cDNA libraries (under construction) *cDNA (dated 11 April 2008) with orthologs in 5 vertebrates (human, opossum, chicken, frog, fugu)

Proper citation: Elephant shark genome sequencing (RRID:SCR_013158) Copy   

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http://www.physionet.org/mimic2/index.shtml

MIMIC II (Multiparameter Intelligent Monitoring in Intensive Care) Database contains comprehensive clinical data from tens of thousands of Intensive Care Unit (ICU) patients. Data were collected between 2001 and 2008 from a variety of ICUs (medical, surgical, coronary care, and neonatal) in a single tertiary teaching hospital. The database contains clinical data from bedside workstations as well as hospital archives. The database also includes thousands of records of continuous high-resolution physiologic waveforms and minute-by-minute numeric time series (trends) of physiologic measurements.

Proper citation: MIMIC II (RRID:SCR_013237) Copy   

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http://epgd.biosino.org/EPGD/

THIS RESOURCE IS NO LONGER IN SERVICE, documented August 23, 2016. EPGD isfocused on the paralogs and the duplication events in the evolution. It is gene-centered and organized by paralog family. The paralog families and paralogons can be searched by text or sequence, and are downloadable from the website in plain text files. The database will be very useful for both experimentalists and bioinformaticians for the study of duplication events or paralog families.

Proper citation: EPGD (RRID:SCR_013364) Copy   

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http://bioinformatics.charite.de/jail

JAIL is a database that classifies the interfaces between domain architectures and those between protein chains and between proteins and nucleic acids. Interacting proteins are difficult to crystallize and rarely present within the Protein Data Base. Nevertheless, it is essential to analyze the interacting parts of the proteins to understand the process of protein-protein docking. To overcome this problem we have built up the JAIL database. Since interacting domains exhibit similar structural features than proteins, all known interfaces between interacting domains of the SCOP database were extracted and classified in JAIL. Only a part of all protein structures are included in SCOP. Particularly, new PDB entries are not yet annotated. To overcome this problem additionally all interfaces between protein chains were calculated and included in the database. This type of interface also comprises the interacting parts of the assumed biological units. The last important type of interfaces provided here is composed of the interacting parts between proteins and nucleic acids. Overall the data set consists of about 180,000 interfaces. JAIL is a comfortable tool to browse through the interface library and to analyze single interfaces. However, more general questions require large-scale analysis. For this purpose, a detailed form enables the compiling of comprehensive non redundant data sets for download.

Proper citation: JAIL- Just Another Interface Library (RRID:SCR_013366) Copy   

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http://www.treefam.org

A database of phylogenetic trees of animal genes. It aims at developing a curated resource that gives reliable information about ortholog and paralog assignments, and evolutionary history of various gene families. TreeFam defines a gene family as a group of genes that evolved after the speciation of single-metazoan animals. It also tries to include outgroup genes like yeast (S. cerevisiae and S. pombe) and plant (A. thaliana) to reveal these distant members.TreeFam is also an ortholog database. Unlike other pairwise alignment based ones, TreeFam infers orthologs by means of gene trees. It fits a gene tree into the universal species tree and finds historical duplications, speciations and losses events. TreeFam uses this information to evaluate tree building, guide manual curation, and infer complex ortholog and paralog relations.The basic elements of TreeFam are gene families that can be divided into two parts: TreeFam-A and TreeFam-B families. TreeFam-B families are automatically created. They might contain errors given complex phylogenies. TreeFam-A families are manually curated from TreeFam-B ones. Family names and node names are assigned at the same time. The ultimate goal of TreeFam is to present a curated resource for all the families. phylogenetic tree, animal, vertebrate, invertebrate, gene, ortholog, paralog, evolutionary history, gene families, single-metazoan animals, outgroup genes like yeast (S. cerevisiae and S. pombe), plant (A. thaliana), historical duplications, speciations, losses, Human, Genome, comparative genomics

Proper citation: Tree families database (RRID:SCR_013401) Copy   

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http://tubic.tju.edu.cn/greglist/

A database listing potential G-quadruplex regulated genes. G-rich DNA sequences can form G-quadruplexes, a four-stranded structure that is stabilized by planar arrays of four guanines associated with hydrogen bonds. Promoter G-quadruplexes have emerged as a new way to regulate gene transcription, such as in c-MYC expression. Further, G-quadruplex motifs are highly enriched in gene promoter regions in humans and other mammals. Greglist contains genes whose promoter regions have G-quadruplex motifs, and these genes are highly likely to be regulated by G-quadruplexes.

Proper citation: Greglist (RRID:SCR_013407) Copy   

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http://urgi.versailles.inra.fr/OryzaTagLine/

Oryza Tag Line consists in a searchable database developed under the Oracle management system integrating phenotypic data resulting from the evaluation of the Génoplante rice insertion line library. To display the sequence information (Flanking Sequence Tags) resulting from the molecular characterization of the mutagen insertion sites in the collection, Oryza Tag Line is linked to OryGenesDB a GGB-derived interface or FLAGDB++ a Java based interface. Aside from generic data ( production record and seed stock ) Oryza Tag Line includes textual and pictorial information resulting from the following observations: (i.) GUS/GFP expression assays conducted on the primary transformants (T0) and/or T1 progenies (ii.) morpho-physiological alterations detected during the growth of the T1 progenies either in phytotron -up to the 5-6 leaf stage- or under agronomical conditions in the field (collaboration with CIAT, Cali, Colombia).

Proper citation: Oryza Tag Line (RRID:SCR_013254) Copy   

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http://plantsp.sdsc.edu

A database of plant protein kinases and phosphatases as well as genomic information for these enzymes. Because protein kinases and phosphatases control so many processes in plants, and occur in networks that unite different cellular processes, a genome wide approach is needed to make significant advances in discovering the roles of these enzymes in the regulation of plant function.

Proper citation: PlantsP (RRID:SCR_013256) Copy   

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http://genome.imim.es/cgi-bin/u12db/u12db.cgi

This is a searchable database of U12-type introns. U12-type introns are spliced by the U12-dependent spliceosome and are present in the genomes of many higher eukaryotic lineages including plants, chordates and some invertebrates. Investigations into the evolution and mechanism of U12-depending splicing would be facilitated by access to a catalog of such introns. However, due to their relatively recent discovery and a systematic bias against recognition of non-canonical splice sites in general, the introns defined by U12-type splice sites are under-represented in genome annotations. Such under-representation compounds the already difficult problem of determining gene structures. It also impedes attempts to study these introns genome-wide or phylum-wide. The resource described here, the U12 Intron Database (U12DB), aims to catalog the U12 introns of completely sequenced eukaryotic genomes and associate orthologous introns with each other.Two pathways for the removal of eukaryotic spliceosomal introns exist: a major pathway that is dependent on the main U2 snRNA-containing spliceosome and a minor pathway that is dependent on the low abundance U12 snRNA-containing spliceosome. The two spliceosomes share only one snRNA, U5, but have many of the same protein components in common. They are distinguished mainly by the splice signal sequences in the pre-mRNA to which they bind. U12 consensus sequences for the donor site, RTATCCTTT, and branch point, TTCCTTRAY, are highly conserved and distinct from the U2 consensi. The two spliceosomes also differ in the order of spliceosomal assembly. U11 and U12 form a dimer which then recognizes the donor site and branch point simultaneously, whereas U1 and U2 recognize these sites independently before associating.Computational scans for U12 introns have previously been performed for human (Levine and Durbin, 2001) and Arabidopsis (Zhu and Brendel, 2003). Both scans used similar methodology, essentially predicting introns and confirming them using alignment to expressed sequence. We extended this approach to 20 genomes using spliced alignment of sequence flanking known introns or transcript-confirmed intron predictions to the genomic sequence of orthologous genes. Details can be found in forthcoming article in the Nucleic Acids Research database issue.

Proper citation: U12DB: The U12 Intron Database (RRID:SCR_013410) Copy   

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http://www.physionet.org/physiobank/database/umwdb/

Stride interval fluctuations were studied in ten young, healthy men. Participants had no history of any neuromuscular, respiratory or cardiovascular disorders, and were taking no medications. Mean age was 21.7 years (range: 18-29 years). Height was 1.77 ���� 0.08 meters (mean ���� S.D.) and weight was 71.8 ���� 10.7 kg. All subjects provided informed written consent. Subjects walked continuously on level ground around an obstacle free, long (either 225 or 400 meters), approximately oval path and the stride interval was measured using ultra-thin, force sensitive switches taped inside one shoe. For more details, please see the accompanying publication. Each subject was given an arbitrary id (si01, si02, ... si10). For each subject, there are six data files: normal (.norm), slow (.slow) and fast (.fast) walking for 1 hour each as well as walking in time to a metronome at normal (.metnrm), slow (.metslw) and fast (.metfst) paces.

Proper citation: Long-term Recordings of Gait Dynamics: Unconstrained and Metronomic Walking (RRID:SCR_013258) Copy   

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http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi

Genetic Codes is a summary resource of the taxonomy of each record and assignment of the correct genetic code for every entry in the GenBank database. GenBank format by historical convention displays mRNA sequences using the DNA alphabet. Thus, for the convenience of people reading GenBank records, the genetic code tables shown here use T instead of U. The following genetic codes are described here: The Standard Code The Vertebrate Mitochondrial Code The Yeast Mitochondrial Code The Mold, Protozoan, and Coelenterate Mitochondrial Code and the Mycoplasma/Spiroplasma Code The Invertebrate Mitochondrial Code The Ciliate, Dasycladacean and Hexamita Nuclear Code The Echinoderm and Flatworm Mitochondrial Code The Euplotid Nuclear Code The Bacterial, Archaeal and Plant Plastid Code The Alternative Yeast Nuclear Code The Ascidian Mitochondrial Code The Alternative Flatworm Mitochondrial Code Blepharisma Nuclear Code Chlorophycean Mitochondrial Code Trematode Mitochondrial Code Scenedesmus Obliquus Mitochondrial Code Thraustochytrium Mitochondrial Code

Proper citation: Genetic Codes (RRID:SCR_013092) Copy   

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http://mordred.bioc.cam.ac.uk/bipa

A database for protein-nucleic acid interaction that provides various features of protein-nucleic acid interfaces.
There are 2333 protein-nucleic acid PDB complexes, 9547 SCOP domains, and 9633 domain-nucleic acid interfaces in BIPA. BIPA also provides a multiple structural alignment of representative structures at the SCOP family level using the program SALIGN, and the structural alignments were further annotated using the program JOY to detect local environments of amino acids.

Proper citation: Biological Interaction database for Protein-nucleic Acid (RRID:SCR_013371) Copy   

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http://yayoi.kansai.jaea.go.jp/colisnp

ColiSNP is a website made up of two databases focused on SNPS. The first database is a database of Single Nucleotide Polymorphism (SNP) located in the protein coding region, and the second is a database of Single Nucleotide Polymorphism (SNP) located in the gene regulation region. The database of Single Nucleotide Polymorphism (SNP) located in the protein coding region is a database of Single Nucleotide Polymorphism (SNP) mapped on protein structure. Users can search the data of SNP on this web site and display the structure of protein with SNP by RasMol. The database of Single Nucleotide Polymorphism (SNP) located in the gene regulation region is a database of Single Nucleotide Polymorphism (SNP) mapped on regulation region. Users can search genes mapped snp on regulation region.

Proper citation: ColiSNP: Database of Single Nucleotide Polymorphism (RRID:SCR_013100) Copy   

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http://cdna01.dna.affrc.go.jp/PIPE

A unification tool which dynamically collects and compiles data from scientific databases in National Institute of Agrobiological Sciences (NIAS), and thereby attempts to encapsulate the genetics and molecular biology of genes from the genomes of Oryza sativa into easy to navigate. The mission of Rice PIPELINE is to provide a unique scientific resource of rice that pools publicly available data commonly sought after for any clone sequence, clone name, GenBank accession number, or keyword.

Proper citation: Rice Pipeline (RRID:SCR_013344) Copy   

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http://bioinf.uta.fi/BTKbase/

A mutation registry for X-linked agammaglobulinemia (XLA). BTKbase lists mutation entries of 1,111 patients from 973 unrelated families showing 602 unique molecular events. Agammaglobulinemia is characterized by failure to produce mature B lymphocyte cells and is associated with a failure of Ig heavy chain rearrangement. Two thirds of cases are familial, and one third of cases are believed to arise from new mutations. Mutations of the BTK gene are found in approximately 80% of patients with agammaglobulinemia. The localization of the mutations on the gene and protein for BTK can be analyzed by clicking sequences on the web pages. It includes a mutation browser, which gives users access to mutations in Bruton tyrosine kinase (BTK) protein sequences, and XLA fact file, and forms for users to submit mutation to the dataset.

Proper citation: BTKbase (RRID:SCR_013101) Copy   

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http://dorina.mdc-berlin.de/rbp_browser/dorina.html

In animals, RNA binding proteins (RBPs) and microRNAs (miRNAs) post-transcriptionally regulate the expression of virtually all genes by binding to RNA. Recent advances in experimental and computational methods facilitate transcriptome-wide mapping of these interactions. It is thought that the combinatorial action of RBPs and miRNAs on target mRNAs form a post-transcriptional regulatory code. We provide a database that supports the quest for deciphering this regulatory code. Within doRiNA, we are systematically curating, storing and integrating binding site data for RBPs and miRNAs. Users are free to take a target (mRNA) or regulator (RBP and/or miRNA) centric view on the data. We have implemented a database framework with short query response times for complex searches (e.g. asking for all targets of a particular combination of regulators). All search results can be browsed, inspected and analyzed in conjunction with a huge selection of other genome-wide data, because our database is directly linked to a local copy of the UCSC genome browser. At the time of writing, doRiNA encompasses RBP data for the human, mouse and worm genomes. For computational miRNA target site predictions, we provide an update of PicTar predictions.

Proper citation: doRiNA (RRID:SCR_013222) Copy   

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http://zope.bioinfo.cnio.es/plan2l/plan2l.html

A web-based online search system that integrates text mining and information extraction techniques to access systematically information useful for analyzing genetic, cellular and molecular aspects of the plant model organism Arabidopsis thaliana. The system facilitates a more efficient retrieval of information relevant to heterogeneous biological topics, from implications in biological relationships at the level of protein interactions and gene regulation, to sub-cellular locations of gene products and associations to cellular and developmental processes, i.e. cell cycle, flowering, root, leaf and seed development. Beyond single entities, also predefined pairs of entities can be provided as queries for which literature-derived relations together with textual evidences are returned.

Proper citation: PLAN2L (RRID:SCR_013346) Copy   

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http://www.gallartinternet.com/mai/

THIS RESOURCE IS NO LONGER IN SERVICE, documented September 13, 2016. A searchable biotechnology database e-books with information on more than 9000 monoclonal antibodies. This database has antibodies produced for the diagnosis and therapy of human cancer, Alzheimer's disease, AIDS, and other diseases as well as for biomarker and proteomics research. Information such as antibody name, species, type, characteristics, antigen characteristics, and developer or distributor of antibody as well as mentions in journals, patents, abstracts and reports up until 2012 are included.

Proper citation: Monoclonal Antibody Index (RRID:SCR_013227) Copy   

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http://orygenesdb.cirad.fr/

The Oryza sativa database displays sequence information resulting from the research of the Centre de cooperation internationale en recherche agronomique pour le developpement. It also includes related molecular data from external rice molecular resources (cDNA full length, Gene, EST, Markers, Expression data, etc.). Genome Browser (Gbrowse), a Web-based application for displaying genomic annotations and other features, is the core of our database. The reference annotation layer consists in the 12 rice pseudomolecules released by the TIGR (Version 5.0, January 2007). All the data are superposed as annotations layers and positioned with respect to these pseudomolecules. We developed a set of tools around GBrowse to retrieve as exhaustively as possible information related to queries with several starting points. These tools allow a molecular geneticist to readily find insertion lines (T-DNA, Tos17, Ds) in genes of interest and to retrieve all the associated annotations related to these sequences.

Proper citation: OryGenesDB (RRID:SCR_013226) Copy   

•   Source: SciCrunch Registry