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http://www.mbio.ncsu.edu/RNaseP/home.html

Ribonuclease P is responsible for the 5''-maturation of tRNA precursors. Ribonuclease P is a ribonucleoprotein, and in bacteria (and some Archaea) the RNA subunit alone is catalytically active in vitro, i.e. it is a ribozyme. The Ribonuclease P Database is a compilation of ribonuclease P sequences, sequence alignments, secondary structures, three-dimensional models and accessory information. The database contains information on bacterial, archaeal, and eukaryotic RNase P. The RNase P and protein sequences are available from phylogentically-arranged lists, individual sequences, or aligned in GenBank format. The database also provides secondary structures and 3D models, as well as movies, still images, and other accessory information.

Proper citation: RNase P Database (RRID:SCR_006680) Copy   

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http://bond.unleashedinformatics.com/

THIS RESOURCE IS NO LONGER IN SERVICE, documented May 10, 2017. A pilot effort that has developed a centralized, web-based biospecimen locator that presents biospecimens collected and stored at participating Arizona hospitals and biospecimen banks, which are available for acquisition and use by researchers. Researchers may use this site to browse, search and request biospecimens to use in qualified studies. The development of the ABL was guided by the Arizona Biospecimen Consortium (ABC), a consortium of hospitals and medical centers in the Phoenix area, and is now being piloted by this Consortium under the direction of ABRC. You may browse by type (cells, fluid, molecular, tissue) or disease. Common data elements decided by the ABC Standards Committee, based on data elements on the National Cancer Institute''s (NCI''s) Common Biorepository Model (CBM), are displayed. These describe the minimum set of data elements that the NCI determined were most important for a researcher to see about a biospecimen. The ABL currently does not display information on whether or not clinical data is available to accompany the biospecimens. However, a requester has the ability to solicit clinical data in the request. Once a request is approved, the biospecimen provider will contact the requester to discuss the request (and the requester''s questions) before finalizing the invoice and shipment. The ABL is available to the public to browse. In order to request biospecimens from the ABL, the researcher will be required to submit the requested required information. Upon submission of the information, shipment of the requested biospecimen(s) will be dependent on the scientific and institutional review approval. Account required. Registration is open to everyone.. Documented on August 19,2019.BOND, which requires registration of a free account, is a resource used to perform cross-database searches of available sequence, interaction, complex and pathway information. BOND integrates a range of component databases including GenBank and BIND, the Biomolecular Interaction Network Database. BOND contains 70+ million biological sequences, 33,000 structures, 38,000 GO terms, and over 200,000 human curated interactions contained in BIND, and is open access. BOND serves the interests of the developing global interactome effort encompassing the genomic, proteomic and metabolomic research communities. BOND is the first open access search resource to integrate sequence and interaction information. BOND integrates BLAST functionality, and contains a well-documented API. BOND also stores annotation links for sequences, including links to Genome Ontology descriptions, MedLine abstracts, taxon identifiers, associated structures, redundant sequences, sequence neighbors, conserved domains, data base cross-references, Online Mendalian Inheritance in Man identifiers, LocusLink identifiers and complete genomes. BIND on BOND The Biomolecular Interaction Network Database (BIND), a component database of BOND, is a collection of records documenting molecular interactions. The contents of BIND include high-throughput data submissions and hand-curated information gathered from the scientific literature. BIND is an interaction database with three classifications for molecular associations: molecules that associate with each other to form interactions, molecular complexes that are formed from one or more interaction(s) and pathways that are defined by a specific sequence of two or more interactions.Interactions A BIND record represents an interaction between two or more objects that is believed to occur in a living organism. A biological object can be a protein, DNA, RNA, ligand, molecular complex, gene, photon or an unclassified biological entity. BIND records are created for interactions which have been shown experimentally and published in at least one peer-reviewed journal. A record also references any papers with experimental evidence that support or dispute the associated interaction. Interactions are the basic units of BIND and can be linked together to form molecular complexes or pathways. The BIND interaction viewer is a tool to visualize and analyze molecular interactions, complexes and pathways. The BIND interaction viewer uses Ontoglyphs to display information about a protein via attributes such as molecular function, biological process and sub-cellular localization. Ontoglyphs allow to graphically and interactively explore interaction networks, by visualizing interactions in the context of 34 functional, 25 binding specificity and 24 sub-cellular localization Ontoglyphs categories. We will continue to provide an open access version of BOND, providing its subscribers with free, unlimited access to a core content set. But we are confident you will soon want to upgrade to BONDplus.

Proper citation: Biomolecular Object Network Databank (RRID:SCR_007433) Copy   

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http://biobases.ibch.poznan.pl/5SData/

A database on nucleotide sequences of 5S rRNAs and their genes. The database contains 1985 primary structures of 5S rRNA and 5S rDNA, and was last updated in 2002, according to the website. They include 60 archaebacterial, 470 eubacterial, 63 plastid, nine mitochondrial and 1383 eukaryotic sequences. The nucleotide sequences of the 5S rRNAs or 5S rDNAs are divided according to the taxonomic position of the source organisms. The sequences for particular organisms can be retrieved as single files using a taxonomic browser or in multiple sequence structural alignments. The multiple sequence alignments of 5S ribosomal RNAs can be downloaded in TAB-delimited and FASTA formats.

Proper citation: 5S Ribosomal RNA Database (RRID:SCR_007545) Copy   

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http://www.ebi.ac.uk/genomes

The EBI genomes pages give access to a large number of complete genomes including bacteria, archaea, viruses, phages, plasmids, viroids and eukaryotes. Methods using whole genome shotgun data are used to gain a large amount of genome coverage for an organism. WGS data for a growing number of organisms are being submitted to DDBJ/EMBL/GenBank. Genome entries have been listed in their appropriate category which may be browsed using the website navigation tool bar on the left. While organelles are all listed in a separate category, any from Eukaryota with chromosome entries are also listed in the Eukaryota page. Within each page, entries are grouped and sorted at the species level with links to the taxonomy page for that species separating each group. Within each species, entries whose source organism has been categorized further are grouped and numbered accordingly. Links are made to: * taxonomy * complete EMBL flatfile * CON files * lists of CON segments * Project * Proteomes pages * FASTA file of Proteins * list of Proteins

Proper citation: EBI Genomes (RRID:SCR_002426) Copy   

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http://www.broad.mit.edu/annotation/fungi/fgi/

Produces and analyzes sequence data from fungal organisms that are important to medicine, agriculture and industry. The FGI is a partnership between the Broad Institute and the wider fungal research community, with the selection of target genomes governed by a steering committee of fungal scientists. Organisms are selected for sequencing as part of a cohesive strategy that considers the value of data from each organism, given their role in basic research, health, agriculture and industry, as well as their value in comparative genomics.

Proper citation: Fungal Genome Initiative (RRID:SCR_003169) Copy   

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http://www.sanger.ac.uk/Projects/Fungi/

Fungal genomes available from the Sanger Institute. Data are accessible in a number of ways; for each organism there is a BLAST server, allowing search of the sequences. Sequences can also be down-loaded directly by FTP. In addition, for those organisms being sequenced using a cosmid approach, finished and annotated cosmids are submitted to EMBL and other public databases.

Proper citation: Fungi Sequencing Projects (RRID:SCR_008524) Copy   

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http://linux1.softberry.com/spldb/SpliceDB.html

Database of canonical and non-canonical mammalian splice sites. The information about verified splice site sequences for canonical and non-canonical sites is presented with the supporting evidence. Weight matrices were built for the major splice groups, which can be incorporated into gene prediction programs.

Proper citation: SpliceDB (RRID:SCR_006262) Copy   

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http://www.kazusa.or.jp/kaos/

This site has been developed by Kazusa DNA Research Institute for the purpose of offering the science community the analyzed sequence data produced by a multi-national Arabidopsis genome sequencing project coordinated by the Arabidopsis Genome Initiatives (AGI). The aim of this service is to enable users to browse the annotated sequence data produced by all the sequencing teams of AGI through an user-friendly graphic display system and search engines. Gene structures proposed on the annotated sequences as well as those predicted by computer programs are presented and each graphic item has a hyperlink to detailed information of the corresponding area. The nucleotide sequence data deposited in GenBank by AGI was downloaded, re-computer-analyzed at Kazusa and parsed results are displayed graphically.

Proper citation: Kazusa Arabidopsis data opening site (RRID:SCR_013511) Copy   

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http://viewer.shigen.info/cgi-bin/crispr/crispr.cgi

Web tool to show micro homology sequences striding over double strand break point created by CRISPR/Cas9 system. Used to search for CRISPR target site with micro-homology sequences. Used to predict deletion pattern.

Proper citation: NBRP Medaka CRISPR target site (RRID:SCR_018159) Copy   

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http://mirwalk.umm.uni-heidelberg.de/

Software tool to store the predicted and the experimentally validated microRNA (miRNA)-target interaction pairs. Predictions within the complete sequence of genes of human, mouse, and rat genomes. Integrates a comparative platform of miRNA-binding sites resulting from ten different prediction datasets.

Proper citation: miRWalk (RRID:SCR_016509) Copy   

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http://www.grt.kyushu-u.ac.jp/spad/

It is divided to four categories based on extracellular signal molecules (Growth factor, Cytokine, and Hormone) and stress, that initiate the intracellular signaling pathway. SPAD is compiled in order to describe information on interaction between protein and protein, protein and DNA as well as information on sequences of DNA and proteins. There are multiple signal transduction pathways: cascade of information from plasma membrane to nucleus in response to an extracellular stimulus in living organisms. Extracellular signal molecule binds specific intracellular receptor, and initiates the signaling pathway. Now, there is a large amount of information about the signaling pathway which controls the gene expression and cellular proliferation. We have developed an integrated database SPAD to understand the overview of signaling transduction.

Proper citation: Signaling Pathway Database (RRID:SCR_008243) Copy   

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http://pbil.univ-lyon1.fr/databases/homolens.php

Database of homologous genes from Ensembl organisms, structured under ACNUC sequence database management system. It allows to select sets of homologous genes among species, and to visualize multiple alignments and phylogenetic trees. It is possible to search for orthologous genes in a wide range of taxons. HOMOLENS is particularly useful for comparative sequence analysis, phylogeny and molecular evolution studies. More generally, HOMOLENS gives an overall view of what is known about a peculiar gene family. Note that HOMOLENS is split into two databases on this server: HOMOLENS contains the protein sequences while HOMOLENSDNA contains the nucleotide sequences. Protein sequences of HOMOLENS have been generated by translating the CDS of HOMOLENSDNA and using associated cross-references to generate the annotations.

Proper citation: Homologous Sequences in Ensembl Animal Genomes (RRID:SCR_008356) Copy   

•   Source: SciCrunch Registry

http://www.primervfx.com/#welcome

PrimerParadise is an online PCR primer database for genomics studies. The database contains predesigned PCR primers for amplification of exons, genes and SNPs of almost all sequenced genomes. Primers can be used for genome-wide projects (resequencing, mutation analysis, SNP detection etc). The primers for eukaryotic genomes have been tested with e-PCR to make sure that no alternative products will be generated. Also, all eukaryotic primers have been filtered to exclude primers that bind excessively throughout the genome. Genes are amplified as amplicons. Amplicons are defined as only one genes exons containing maximaly 3000 bp long dna segments. If gene is longer than 3000 bp then it is split into the segments at length 3000 bp. So for example gene at length 5000 bp is split into two segment and for both segments there were designed a separate primerpair. If genes exons length is over 3000 bp then it is split into amplicons as well. Every SNP has one primerpair. In addition of considering repetitive sequences and mono-dinucleotide repeats, we avoid designing primers to genome regions which contain other SNPs. -There are two ways to search for primers: you can use features IDs ( for SNP primers Reference ID, for gene/exon primers different IDs (Ensembl gene IDs, HUGO IDs for human genes, LocusLink IDs, RefSeq IDs, MIM IDs, NCBI gene names, SWISSPROT IDs for bacterial genes, VEGA gene IDs for human and mouse, Sanger S.pombe systematic gene names and common gene names, S.cerevisiae GeneBanks Locus, AccNo, GI IDs and common gene names) -you can use genome regions (chromosome coordinates, chromosome bands if exists) -Currently we provide 3 primers collections: proPCR for prokaryotic organisms genes primers -euPCR for eukaryotic organisms genes/exons primers -snpPCR for eukaryotic organisms SNP primers Sponsors: PrimerStudio is funded by the University of Tartu.

Proper citation: PrimerStudio (RRID:SCR_008232) Copy   

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http://alizadehlab.stanford.edu/

This is an open-source Mouse Exonic Evidence-Based Oligonucleotide Chip (MEEBOChip), and are in the process of building the human counterpart, HEEBOChip. The set of 70mers for MEEBOChip is already available from Illumina, Inc., with synthesis of HEEBOChip 70mers in progress. Both arrays are based on a novel selection of exonic long-oligonucleotides (70-mers) from a genomic annotation of the corresponding complete genome sequences, using a transcriptome-based annotation of exon structure for each genomic locus. Using a combination of existing and custom-tailored tools and datasets (including millions of mRNA and EST sequences), we built and performed a systematic examination of transcript-supported exon structure for each genomic locus at the base-pair level (i.e., exonic evidence). This strategy allowed them to select both constitutive and in many cases alternative exons for nearly every gene in the corresponding genome (e.g., protocadherin locus), allowing an unprecedented exploration of human and mouse biology. Furthermore, they used experimentally derived data to hone the selection of these 70mers, helping maximize their performance under typical fluorescent labeling and hybridization conditions. Specifically, they applied and refined the ArrayOligoSelector algorithm from Joe DeRisis laboratory to select 70mers, considering not only their uniqueness (i.e., hybridization specificity) within the content of the entire genome, but also to overcome the known biases of labeling and hybridization methods (e.g., 3-biased reverse transcription and in vitro transcription reactions).

Proper citation: Alizadehlab: MeeboChip and HeeboChip Open Source Project (RRID:SCR_008384) Copy   

•   Source: SciCrunch Registry

http://mips.gsf.de/services/genomes/uwe25/

THIS RESOURCE IS NO LONGER IN SERVICE, documented on July 15, 2013. This is the official database of the environmental chlamydia genome project. This resource provides access to finished sequence for Parachlamydia-related symbiont UWE25 and to a wide range of manual annotations, automatical analyses and derived datasets. Functional classification and description has been manually annotated according to the Annotation guidelines. Chlamydiae are the major cause of preventable blindness and sexually transmitted disease. Genome analysis of a chlamydia-related symbiont of free-living amoebae revealed that it is twice as large as any of the pathogenic chlamydiae and had few signs of recent lateral gene acquisition. We showed that about 700 million years ago the last common ancestor of pathogenic and symbiotic chlamydiae was already adapted to intracellular survival in early eukaryotes and contained many virulence factors found in modern pathogenic chlamydiae, including a type III secretion system. Ancient chlamydiae appear to be the originators of mechanisms for the exploitation of eukaryotic cells. Environmental chlamydiae have recently been recognized as obligate endosymbionts of free-living amoebae and have been implicated as potential human pathogens. Environmental chlamydiae form a deep branching evolutionary lineage within the medically important order Chlamydiales. Despite their high diversity and ubiquitous distribution in clinical and environmental samples only limited information about genetics and ecology of these microorganisms is available. The Parachlamydia-related Acanthamoeba symbiont UWE25 was therefore selected as representative environmental chlamydia strain for whole genome sequencing. Comparative genome analysis was performed using PEDANT and simap. Sponsors: The environmental chlamydia genome project was funded by the bmb+f (German Federal Ministry of Education and Research) and is part of the Competence Network PathoGenoMiK.

Proper citation: Protochlamydia amoebophila UWE25 (RRID:SCR_008222) Copy   

•   Source: SciCrunch Registry

http://HIVBrainSeqDB.org

The HIV Brain Sequence Database (HIVBrainSeqDB) is a public database of HIV envelope sequences, directly sequenced from brain and other tissues from the same patients. For inclusion in the database, sequences must: (i) be deposited in Genbank; (ii) include some portion of the HIV env region; (iii) be clonal, amplified directly from tissue; and (iv) be sampled from the brain, or sampled from a patient for which the database already contains brain sequence. Sequences are annotated with clinical data including viral load, CD4 count, antiretroviral status, neurocognitive impairment, and neuropathological diagnosis, all curated from the original publication. Tissue source is coded using an anatomical ontology, the Foundational Model of Anatomy, to capture the maximum level of detail available, while maintaining ontological relationships between tissues and their subparts. 44 tissue types are represented within the database, grouped into 4 categories: (i) brain, brainstem, and spinal cord; (ii) meninges, choroid plexus, and CSF; (iii) blood and lymphoid; and (iv) other (bone marrow, colon, lung, liver, etc). Currently, the database contains 2517 envelope sequences from 90 patients, obtained from 22 published studies. 1272 sequences are from brain; the remaining 1245 are from blood, lymph node, spleen, bone marrow, colon, lung and other non-brain tissues. The database interface utilizes a faceted interface, allowing real-time combination of multiple search parameters to assemble a meta-dataset, which can be downloaded for further analysis. This online resource will greatly facilitate analysis of the genetic aspects of HIV macrophage tropism, HIV compartmentalization and evolution within the brain and other tissue reservoirs, and the relationship of these findings to HIV-associated neurological disorders and other clinical consequences of HIV infection.

Proper citation: HIV Brain Sequence Database (RRID:SCR_008819) Copy   

•   Source: SciCrunch Registry

http://mips.gsf.de/genre/proj/ustilago/

The MIPS Ustilago maydis Genome Database aims to present information on the molecular structure and functional network of the entirely sequenced, filamentous fungus Ustilago maydis. The underlying sequence is the initial release of the high quality draft sequence of the Broad Institute. The goal of the MIPS database is to provide a comprehensive genome database in the Genome Research Environment in parallel with other fungal genomes to enable in depth fungal comparative analysis. The specific aims are to: 1. Generate and assemble Whole Genome Shotgun sequence reads yielding 10X coverage of the U. maydis genome 2. Integrate the genomic sequence assembly with physical maps generated by Bayer CropScience 3. Perform automated annotation of the sequence assembly 4. Align the strain 521 assembly with the FB1 assembly provided by Exelixis 5. Release the sequence assembly and results of our annotation and analysis to public Ustilago maydis is a basidiomycete fungal pathogen of maize and teosinte. The genome size is approximately 20 Mb. The fungus induces tumors on host plants and forms masses of diploid teliospores. These spores germinate and form haploid meiotic products that can be propagated in culture as yeast-like cells. Haploid strains of opposite mating type fuse and form a filamentous, dikaryotic cell type that invades plant tissue to reinitiate infection. Ustilago maydis is an important model system for studying pathogen-host interactions and has been studied for more than 100 years by plant pathologists. Molecular genetic research with U. maydis focuses on recombination, the role of mating in pathogenesis, and signaling pathways that influence virulence. Recently, the fungus has emerged as an excellent experimental model for the molecular genetic analysis of phytopathogenesis, particularly in the characterization of infection-specific morphogenesis in response to signals from host plants. Ustilago maydis also serves as an important model for other basidiomycete plant pathogens that are more difficult to work with in the laboratory, such as the rust and bunt fungi. Genomic sequence of U. maydis will also be valuable for comparative analysis of other fungal genomes, especially with respect to understanding the host range of fungal phytopathogens. The analysis of U. maydis would provide a framework for studying the hundreds of other Ustilago species that attack important crops, such as barley, wheat, sorghum, and sugarcane. Comparisons would also be possible with other basidiomycete fungi, such as the important human pathogen C. neoformans. Commercially, U. maydis is an excellent model for the discovery of antifungal drugs. In addition, maize tumors caused by U. maydis are prized in Hispanic cuisine and there is interest in improving commercial production. The complete putative gene set of the Broad Institute''s second release is loaded into the database and in addition all deviating putative genes from a putative gene set produced by MIPS with different gene prediction parameters are also loaded. The complete dataset will then be analysed, gene predictions will be manually corrected due to combined information derived from different gene prediction algorithms and, more important, protein and EST comparisons. Gene prediction will be restricted to ORFs larger than 50 codons; smaller ORFs will be included only if similarities to other proteins or EST matches confirm their existence or if a coding region was postulated by all prediction programs used. The resulting proteins will be annotated. They will be classified according to the MIPS classification catalogue receiving appropriate descriptions. All proteins with a known, characterized homolog will be automatically assigned to functional categories using the MIPS functional catalog. All extracted proteins are in addition automatically analysed and annotated by the PEDANT suite.

Proper citation: MIPS Ustilago maydis Database (RRID:SCR_007563) Copy   

•   Source: SciCrunch Registry

http://mips.gsf.de/simap/

It provides a database based on a pre-computed similarity matrix covering the similarity space formed by >4 million amino acid sequences from public databases and completely sequenced genomes. The database is capable of handling very large datasets and is updated incrementally. For sequence similarity searches and pairwise alignments, we implemented a grid-enabled software system, which is based on FASTA heuristics and the Smith Waterman algorithm. SimpleSIMAP and AdvancedSIMAP retrieve homologs for given protein sequences that need to be contained in the SIMAP database. While SimpleSIMAP provides only selected parameters and preconfigured search spaces, the AdvancedSIMAP allows the user to specify search space, filtering and sorting parameters in a flexible manner. Both types of queries result in lists of homologs that are linked in turn to their homologs. So the web interfaces allow users to explore quickly and interactively the protein world by homology. Sponsors: SIMAP is supported by the Department of Genome Oriented Bioinformatics of the Technische Universitt Mnchen and the Institute for Bioinformatics of the GSF-National Research Center for Environment and Health.

Proper citation: SIMAP (RRID:SCR_007927) Copy   

•   Source: SciCrunch Registry

http://itfp.biosino.org/itfp/

ITFP is an integrated transcription factor (TF) platform, which included abundant TFs and targets message of mammalian. Support vector machine (SVM) algorithm combined with error-correcting output coding (ECOC) algorithm was utilized to identify and classify transcription factor from protein sequence of Human, Mouse and Rat. For transcription factor targets, a reverse engineering method named ARACNE was used to derive potential interaction pairs between transcription factor and downstream regulated gene from Human, Mouse and Rat gene expression profile data. Detailed information of gene expression profile data can be found in help page. Moreover, all data provided by the platform is free for non-commercial users and can be downloaded through links on help page.

Proper citation: Intergrated Transcription Factor Platform (RRID:SCR_008119) Copy   

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http://www.thearkdb.org/arkdb/

This website contains the mapping sequence of poultry. The ArkDB database system aims to provide a comprehensive public repository for genome mapping data from farmed and other animal species. In doing so, it aims to provide a route in to genomic and other sequence from the initial viewpoint of linkage mapping, RH mapping, physical mapping or - possibly more importantly - QTL mapping data. It's supported, in part, by the USDA-CSREES National Animal Genome Research Program in order to serve the poultry genome mapping community. This system represents a complete rewrite of the original version with the code migrated to java and the underlying database targeted at postgres (although any standards-compliant database engine should suffice). The initial release records details of maps and the markers that they contain. There are alternative entry points that target either a chromosome or a specific mapping analysis as the starting point. Limited relationships between markers are recorded and displayed. As with the previous version, all maps are drawn using data extracted from the database on the fly.

Proper citation: ChickBase (RRID:SCR_008147) Copy   

•   Source: SciCrunch Registry