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http://www.sbg.bio.ic.ac.uk/~ino/
A database containing compound microsatellite-SNP markers in human, dog, mouse, rat and chicken. SNPSTRs are a relatively new type of compound genetic marker which combines a STR marker with one or more tightly linked SNPs. This combination of co-inherited markers evolving at different rates may offer the possibility of gaining better resolved insights into population genetic processes compared to when these different marker types are used separately. SNPSTRs were first described by Mountain et al (2002) who developed experimental protocols for autosomal SNPSTRs which contain a SNP and a microsatellite within 500 base pairs apart. microsatellite-SNP, dog microsatellite-SNP, mouse microsatellite-SNP, rat microsatellite-SNP, chicken microsatellite-SNP
Proper citation: SNPSTR (RRID:SCR_007945) Copy
This is a database of human C/D box and H/ACA modification guide RNAs. Information on a particular snoRNA can be accessed by three ways: 1- On the Search page, just type the name of the snoRNA (for example ACA17) in the Id window. 2- The Find guide RNA contains the sequences of the human ribosomal rRNAs 28S, 18S and 5.8S, and of the snRNAs U1, U2, U4, U5 and U6, with the positions of modified (2''O-ribose methylated or pseudo-uridinylated) nucleotides, and the identity of the corresponding modification guide RNAs. You can click on the name of the relevant snoRNA. 3- By utilizing the link to the UCSC Human Genome Browser.
Proper citation: snoRNABase- a comprehensive database of human H/ACA and C/D box snoRNAs. (RRID:SCR_007939) Copy
https://omictools.com/sno-scarnabase-tool
A curated database for small nucleolar RNAs and small cajal body-specific RNAs. It presents sno/scaRNA-associated genetic and functional data and provides access to several other database sources via web-accessible search interfaces. Consisting of 1979 sno/scaRNA records obtained from 85 organisms, sno/scaRNAbase is a combination of systematic literature curation and annotation effort. small nucleolar RNA, small cajal body-specific RNA
Proper citation: Sno/scaRNAbase (RRID:SCR_007938) Copy
http://www.compbio.dundee.ac.uk/SNAPPI/downloads.jsp
An object-oriented database of domain-domain interactions observed in structural data. SNAPPI-DB is a useful resource for any analysis of structures but has been opitmised for analysis on domain-domain interactions and domain-ligand interactions. The database has already been employed for 3 studies on the properties of domain-domain interactions and is currently being employed to train a protein-protein interaction predictor and a functional residue predictor. SNAPPI-DB has several features which are not available in other databases, including links to the MSD, speed, being object oriented, storage of multiple domain definitions, and storage of Protein Quaternary Structures (PQS).
Proper citation: SNAPPI (RRID:SCR_007937) Copy
http://www-deletion.stanford.edu/YDPM/YDPM_index.html
This database contains different yeast strains searchable by ORF and gene name, and serves to support the Yeast Deletion and the Mitochondrial Proteomics Project. The database is hyperlinked with other public databases. The project aims to increase the understanding of mitochondrial function and biogenesis in the context of the cell. In the Deletion Project, strains from the deletion collection were monitored under 9 different media conditions selected for the study of mitochondrial function. 5791 heterozygous diploid and 4706 homozygous diploid deletion strains were monitored in parallel using molecular barcodes on fermentable (YPD, YPDGE) and non-fermentable substrates (YPG, YPE, YPL). The YDPM database contains both the raw data and growth rates calculated for each strain in each media condition. Strains can be searched by ORF or Gene name to access growth measurements and data plots for each strain. Category: Genomics Databases (non-vertebrate) Subcategory: Fungal genome databases Category: Organelle databases Subcategory: Mitochondrial genes and proteins
Proper citation: YDPM - Yeast Deletion Project (RRID:SCR_007977) Copy
A database containing predicted viral miRNA candidate hairpins. Users may query the putative miRNA hairpins of a specific viral species by the hierarchical menu or by search function using the GenBank Identifier or RefSeq accession number. In addition, users can also search for the putative target genes of a particular viral miRNA hairpins by a RNAhybrid service link. We have previously identified human intronic microRNA as well as zebrafish microRNA. The microRNA hairpin discovery pipeline was also applied to discover viral encoded microRNAs. All viral genomes were obtain from NCBI. The classification of virus is based on the taxonomy table of NCBI (Jun, 2006). Totally, the genomes of 2266 viruses were analyzed. The 3’-UTR regions of human, mouse, rat, zebrafish, arabidopsis and rice genes are available for search.
Proper citation: Vir-Mir (RRID:SCR_007971) Copy
Collection of transmembrane protein datasets containing experimentally derived topology information from the literature and from public databases. Web interface of TOPDB includes tools for searching, relational querying and data browsing, visualisation tools for topology data.
Proper citation: Topology Data Bank of Transmembrane Proteins (RRID:SCR_007964) Copy
TassDB stores extensive data about alternative splice events at GYNGYN donors and NAGNAG acceptors. Currently, 114,554 tandem splice sites of eight species are contained in the database, 5,209 of which have EST/mRNA evidence for alternative splicing. Users can search by Transcript Accession Number and Gene Symbol, SQL Query, and Tandem Donor/Tandem Acceptor pairs.
Proper citation: TAndem Splice Site DataBase (RRID:SCR_007961) Copy
TargetDB, a target registration database, provides information on the experimental progress and status of targets selected for structure determination. Search sequences from the PSI Structural Genomics Centers and other Structural Genomics projects.For more information about how these proteins were cloned, expressed, purified, or other experimental protocols please go to the Protein expression, purification, and crystallization DataBase.
Proper citation: TargetDB: Structural Genomics Target Search (RRID:SCR_007960) Copy
http://bioinformatics.ca/links_directory/
Database of curated links to molecular resources, tools and databases selected on the basis of recommendations from bioinformatics experts in the field. This resource relies on input from its community of bioinformatics users for suggestions. Starting in 2003, it has also started listing all links contained in the NAR Webserver issue. The different types of information available in this portal: * Computer Related: This category contains links to resources relating to programming languages often used in bioinformatics. Other tools of the trade, such as web development and database resources, are also included here. * Sequence Comparison: Tools and resources for the comparison of sequences including sequence similarity searching, alignment tools, and general comparative genomics resources. * DNA: This category contains links to useful resources for DNA sequence analyses such as tools for comparative sequence analysis and sequence assembly. Links to programs for sequence manipulation, primer design, and sequence retrieval and submission are also listed here. * Education: Links to information about the techniques, materials, people, places, and events of the greater bioinformatics community. Included are current news headlines, literature sources, educational material and links to bioinformatics courses and workshops. * Expression: Links to tools for predicting the expression, alternative splicing, and regulation of a gene sequence are found here. This section also contains links to databases, methods, and analysis tools for protein expression, SAGE, EST, and microarray data. * Human Genome: This section contains links to draft annotations of the human genome in addition to resources for sequence polymorphisms and genomics. Also included are links related to ethical discussions surrounding the study of the human genome. * Literature: Links to resources related to published literature, including tools to search for articles and through literature abstracts. Additional text mining resources, open access resources, and literature goldmines are also listed. * Model Organisms: Included in this category are links to resources for various model organisms ranging from mammals to microbes. These include databases and tools for genome scale analyses. * Other Molecules: Bioinformatics tools related to molecules other than DNA, RNA, and protein. This category will include resources for the bioinformatics of small molecules as well as for other biopolymers including carbohydrates and metabolites. * Protein: This category contains links to useful resources for protein sequence and structure analyses. Resources for phylogenetic analyses, prediction of protein features, and analyses of interactions are also found here. * RNA: Resources include links to sequence retrieval programs, structure prediction and visualization tools, motif search programs, and information on various functional RNAs.
Proper citation: Bioinformatics Links Directory (RRID:SCR_008018) Copy
http://tbestdb.bcm.umontreal.ca/searches/welcome.php
The taxonomically broad EST database TBestDB serves as a repository for EST data from a wide range of eukaryotes, many of which have previously not been thoroughly investigated. Users can search by annotated name, EC#, and view datasets that contain classification hierarchies for pathways, for reactions (the enzyme nomenclature system), for compounds, and for genes. Most of the data contained in TBestDB has been generated by the labs of the Protist EST Program located in six universities across Canada.
Proper citation: Taxonomically Broad EST Database (RRID:SCR_007962) Copy
http://smartdb.bioinf.med.uni-goettingen.de/
It collects information about scaffold/matrix attached regions and the nuclear matrix proteins that are supposed be involved in the interaction of these elements with the nuclear matrix. It covers the whole range from yeast to human. The SMAR table gives information on individual sequence elements of experimentally proven matrix binding activity. In release 2.3 it contains 500 entries. The sequences therein can be assigned to more than 150 genes from eukaryotic species ranging from yeast to human. The SMARbinder table contains 96 entries (release 2.3), but this figure does not reflect the number of independent S/MAR binding proteins. First of all, homologous factors from different species such as human and mouse SATB1 are given in different entries since they may differ in some aspects. Moreover, products of distinct but very similar genes or alternative splice products are included as separate entries. In some cases a more general term defining a S/MAR-binding activity may appear as one entry eventhough it might be composed of two or more subunits. The SMARbinder table will only contain those proteins of nuclear localization for which an interaction with a well defined S/MAR has been shown. Besides that the SMARbinder table will also include proteins that are proven components of the the salt-resitent (LIS-resistent) nuclear matrix. Gene entries, besides of giving the gene name in a long and a short (abbreviated) denomination, collect all links to individual S/MARs given in S/MARt DB and/or provide pointers to "S/MARbinders". The entries also contain links to transcription factor binding sites listed in TRANSFAC and give a link to the corresponding TRRD entry describing the regulatory features of the gene on different hierarchical levels.
Proper citation: S/MARt DB (RRID:SCR_007910) Copy
http://bioinfo3d.cs.tau.ac.il/RsiteDB/
It is a database that details the interactions of extruded, unpaired RNA nucleotide bases. It presents and classifies the protein binding pockets that accommodate them, and also allows the recognition of similar protein binding patters involved in interactions with different RNA molecules. Given an unbound structure of a target protein, it allows the prediction of its RNA nucleotide binding sites. The goal of this database is to describe, classify, and predict the interactions between protein binding sites and single-stranded RNA bases. Specifically, RsiteDB describes the protein binding pockets that accommodate extruded nucleotides not involved in RNA base pairing. RsiteDB has two modes of operation. Analysis and classification of protein-RNA interactions: Given a protein-RNA complex RsiteDB analyzes its nucleotide and dinucleotide binding sites. It details the properties of the protein binding pockets that accommodate these extruded nucleotides and presents a list of proteins with similar binding pockets. These proteins may have a totally different overall sequences and structural folds. RsiteDB details and visualizes the features shared by all the binding sites classified to the same cluster. Prediction of RNA dinucleotide binding sites: Given a target, potentially unbound, protein structure we search its surface for regions similar to the created 3-D consensus binding patterns of RNA dinucleotides. The recognized regions are predicted to serve as binding sites. Using leave-one-out tests, the success rate of these predictions was estimated to be about 80%. It must be noted that currently we do not aim to predict whether a protein can bind RNA; rather, given an unbound RNA binding protein, our goal is to predict its binding sites and their modes of interaction. In addition, due to a low number of single nucleotide clusters, currently, we do not use them for the prediction.
Proper citation: RsiteDB- RNA binding sites database (RRID:SCR_007906) Copy
http://www.mcponline.org/content/3/10/1009.long
THIS RESOURCE IS NO LONGER IN SERVICE, documented August 19, 2016. Database that offers information on molecules and interactions involving signaling pathways through literature-based curative explanation and laboratory results as well as basic information through links to other databases. Its major content consists of signaling entities and signaling interactions designed to describe various levels of signaling events. It is designed to convey chemical changes and logical information flow in detail through careful data modeling of complex signaling processes. ROSPath was developed for the purpose of aiding the research of ROS-mediated signaling pathways including growth factor-, stress- and cytokine-induced signaling that are main research interests of the Division of Molecular Life Sciences and Center for Cell Signaling Research in Ewha Womans University. ROSPath is designed to describe cellular signaling processes in molecular detail and to accumulate data and knowledge regarding signaling pathways with the organized database structure. It offers useful means to researchers by providing curative Information on the signaling pathways of interest and by providing means of managing data produced by high-throughput experiments such as proteomics and genomics tools. Furthermore, its goal is to provide effective and flexible tools for signaling pathway analysis and data mining by means of extensive data modeling and development of computer-aided tools.
Proper citation: ROSPath- Reactive Oxygen Species Related Signaling Pathway (RRID:SCR_007903) Copy
An integrated database of human coding single nucleotide polymorphisms (SNPs) and their annotations. Unlike other databases of similar nature, apart from integrating several coding SNPs (cSNPs) and protein-related information resources, we predict the implications of the non-synonymous SNPs (nsSNPs) using two well known algorithms (SIFT and PolyPhen). The results are presented in an intuitive visualization that depicts the cSNPs mapped onto protein domains and highlights those nsSNPs that are potentially damaging/deleterious or have been reported as disease allelic variants (based on OMIM). The query interface also supports searching for a list of proteins associated with any gene ontology term, pathway, disease term or gene family. Results can also be downloaded as a spreadsheet. The visualization page also provides links to several other related sources and dynamic links to literature references.
Proper citation: PolyDoms (RRID:SCR_007869) Copy
http://ribosome.med.miyazaki-u.ac.jp/
It is a database that provides detailed information about ribosomal protein (RP) genes. It contains data from humans and other organisms. Users can search this database by gene name and organism. Each record includes sequences (genomic, cDNA, and amino acid sequences), intron/exon structures, genomic locations, and information about orthologs. In addition, users can view and compare the gene structures from different organisms and make multiple amino acid sequence alignments. RPG also provides information on small nucleolar RNAs (snoRNAs) that are encoded in the introns of RP genes.
Proper citation: RPG - Ribosomal Protein Gene database (RRID:SCR_007904) Copy
http://point.bioinformatics.tw/Welcome.do
POINT is a protein-protein interaction database. It includes annotation of interologs and protein phsophorylation. This work analyzes the applicability of orthologs-based PPI prediction and provide the theoretical upper-bound of this approach.
Proper citation: POINT: Prediction Of INTeractome (RRID:SCR_007866) Copy
The UK Crop Plant Bioinformatics Network (UK CropNet) was established in 1996 as part of the BBSRC''s Plant and Animal Genome Analysis special initiative. Our focus is the development, management, and distribution of information relating to comparative mapping and genome research in crop plants. Find out more about our background or read our UK CropNet paper published in Nucleic Acids Research (pdf reader required).This site hosts a wide range of databases and software developed by UK CropNet, as well as hosting many other plant databases developed in the USA. You can perform a keyword text search across all of these databases or use our UK CropNet BLAST server to search against all of the sequences in these databases.
Proper citation: CropNet (RRID:SCR_007987) Copy
A database of mRNA polyadenylation sites. PolyA_DB version 1 contains human and mouse poly(A) sites that are mapped by cDNA/EST sequences. PolyA_DB version 2 contains poly(A) sites in human, mouse, rat, chicken and zebrafish that are mapped by cDNA/EST and Trace sequences. Sequence alignments between orthologous sites are available. PolyA_SVM predicts poly(A) sites using 15 cis elements identified for human poly(A) sites.
Proper citation: PolyA DB (RRID:SCR_007867) Copy
It provides access to results from RNAi interference studies in C. elegans, including images, movies, phenotypes, and graphical maps. RNAiDB contains all published RNAi experiments in C. elegans that have been deposited in WormBase, including data from the literature and published large-scale RNAi studies. RNAi to gene mappings for all experiments have been re-analyzed using ePCR and/or a sliding n-mer window method to identify all genes in different genomic locations that may potentially be inhibited by each experiment. Gene maps showing canonical and putative alternate mappings are displayed graphically on RNAi Experiment and Gene/ORF card pages.
Proper citation: RNAiDB (RRID:SCR_007900) Copy
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