Spectral Database for Organic Compounds SDBS
Provides access to six different types of spectra under a directory of organic compounds. “Spectral Database for Organic Compounds SDBS” contains a major part of commercial chemical reagents into its compounds.
TuMa Rdb / Tumor Markers Reference database
Gathers tumor marker references in several diseases. TuMa Rdb is a repository which provides information related with more than 80 markers curated from about 400 case studies. The platform allows users to query marker by name, possibly in association with a disease of interest, and reports its related diseases, a benchmark as well as the literature reference(s) linked to this specific case.
KAGIANA / Kazusa Arabidopsis Gene Information And Network Analysis
Allows retrieval of summary information about Arabidopsis genes. KAGIANA summarizes various Arabidopsis omics analyses from databases and tools and provides links to pages for genes of interest in databases. The database also provides ‘Tools’ macro programs including ‘Confeito’, ‘GX bar chart’, ‘GO pie chart’ and ‘ATTED chart’. It aims to assist plant biologists in accessing information from omics analyses so that they can incorporate it into their plant biology research.
Assists to find sequences and retrieve annotations data from UCSC Genome Browser. PipHelper produces repeats, sequence and exons files for further processing by PipMaker. User have to select an assembly, enter a position and choose an annotation to use this database.
A Syllabus of Human Hemoglobin Variants
Provides information about known human Hb variants. A Syllabus of Human Hemoglobin Variants contains more than 600 Hb variants. This resource is useful for researchers wishing to better understand the pathophysiology of hemoglobin diseases, develop therapies, or elucidate the dynamics of sequence alterations.
A Syllabus of Thalassemia Mutations
Contains several data about thalassemia alleles and hereditary persistence of fetal hemoglobin (HPFH) determinants.
ARTRA DB / Arabidopsis Transcriptome and DNA MicroArray Database
Provides information about Arabidopsis thaliana sequence. ARTRA DB contains more than 250 000 transcripts sequences of Arabidopsis from Expression Sequence Tags (ESTs).
RISH Database
Provides information about Expressed Sequence Tags (EST) of Trees. RISH Database contains more than 8900 sequences obtained by sequencing a normalized cDNA library of Acacia Mangium.
Provides information about molecular biology topic. DBGET is a database allowing to search and extract entries from a diverse range of databases. In this resource, a database is considered as a collection of entries which can be stored in a single file or multiple files. It is a conceptual extension of IDEAS (Integrated Database and Extended Analysis System) for nucleic acids and protein. This database works jointly to LinkDB.
Supplies data concerning molecular biology. LinkDB is a collection of database links. It contains the original links provided by each database and the indirect and reverse links that are computed. This database works jointly to DBGET.
Consists in a collection of manually drawn pathway maps. KEGG PATHWAY concerns mainly molecular interaction, reaction and relation networks for: (1) drug development; (2) human diseases; (3) organismal systems; (4) cellular processes; (5) environmental information processing; (6) genetic information processing; (7) and metabolism. The identification of each pathway map is made thanks to a combination of 2-4 letter prefix code and 5-digit number.
Provides a collection of lectins and carbohydrates. Glyco-CD offers information on 63 clusters of differentiation (CD) antigens. Lectins and carbohydrates are defined by CD antibodies that are differentially expressed primarily on human leukocytes and also on certain endothelial and epithelial cells. This database is organized into two parts: carbohydrate recognition CD antigens and glycan CDs.
Gathers information about stem cell research. SyStemCell is a manually-curated database which contains data extracted of more than 280 PubMed’ publications. It aims to provide a basic platform to extract relationships suggested by the multisource data. Moreover, it includes an analysis tool to mine potential relationships among different regulation levels and possibly formulate new hypothesis.
Compiles data about the pseudomonas. SYSTOMONAS registers information on eight different Pseudomonas species and strains, which genomes have been completely sequenced and functionally annotated. The database contains information for all levels of analysis as microarray and proteomics data, metabolite measurements, sequence data, gene-regulatory networks (GRNs) and corresponding enzyme data.
SysZNF / the C2H2 zinc finger gene database
Gathers informations about C2H2-ZNF protein coding genes in human and mouse. SysZNF contains (i) arrangements of C2H2 gene information based on physical localization in the respective genome; (ii) downloadable and visual information on gene organization and protein domain composition; (iii) a starting point to search and examine ortholog and paralog relationships in different species and; (iv) direct links from a particular data set to other resources of the scientific community.
Provides information about various strains of Trypanosoma cruzi. TcSNP gathers T. cruzi sequences, multiple sequence alignments (MSAs) obtained from these sequences, single-nucleotide polymorphisms (SNPs) and small indels identified derived from scanning. The database offers text-based searches for sequences based on attributes derived from their annotation. The result provides a list of genes matching the specified criteria, containing links to the corresponding MSAs, where users can visualize polymorphic sites in different colors, typefaces and styles.
TGI / TIGR Gene Index database
Gathers information about publicly available expressed sequence tags (EST) and known gene sequence data stored in GenBank for each target species. TGI contains more than 70 species including animals, plants, fungi and protists. The dataset represents about 50 000 ESTs. Besides, nucleotide or protein sequences can be searched using WU-BLAST against individual TGI databases, eukaryotic gene orthologs (EGO) or pre-selected classes of species, such as animals or plants.
the CEREALAB database / Cereals genotypic phenotypic source
Combines data obtained by genotyping activity of the CEREALAB research group with the already available molecular, genotypic and phenotypic data. The CEREALAB database intends to help the breeders in (i) unravelling the genetics of economically important phenotypic traits; (ii) identifying and choosing molecular markers associated to key traits; (iii) identifying alleles of such markers associated to trait positive variants; and (iv) in choosing the desired parental for breeding programs.
the DARC site / The Database for Aligned Ribosomal Complexes site
Gathers information about Cryo-electron microscopy (cryo-EM) density maps and atomic coordinates of ribosomal particles from Protein Data Bank (PDBs) and Electron Microscopy Data Bank (EMDB). Users can make searches by EMDB or PDB accession number (ID) or use the drop-down menu to restrict the search to Source Database or ID, title, author, abstract or PubMed ID, as well as method, organism, ligand, classification or particle type
The gene-specific codon counting database
Compiles and analyzes codon combinations in all budding yeast genes. The gene-specific codon counting database provides a method for analyzing codon runs in both genes and genomes. The database allows users to visualize bar or combination graphs and to promote data analysis made by them. Besides, it authorizes to export both codon combination and frequency data for user-defined genes or for the entire genome.
The HTLV-1 database
Furnishes a library dealing with annotated HTLV-1 proviral sequences derived from clinical, epidemiological and geographical studies publicly available. The HTLV-1 database contains more than 2000 annotated sequences. Searches can be made by specific search fields, as well as genomic region, subtype, subgroup, geographic region of origin, and continent of origin, to allow various data combinations.
Bird Base
Provides access to information about bird genomes and genomics. Bird Base is a database of avian genes and genomes that also provides gene expression tools.
Provides access to genomics data on Cichlid fishes.
Provides access to information about crocodilians genomes. CrocBase is an online resource that allows users to search for predicted gene information, provides genomes browsers for Alligator mississippiensis, Crocodylus porosus, Gavialis gangeticus as well as Comparative Genomics (CoGe) browser for finding and comparing genomic sequences.
Gathers genomic data from opossums and other American marsupial species. OppossumBase is an online database that contains expressed sequence data (ESTs) from Monodelphis domestica and that also provides several genomics tools. Links to other databases and resources are also available.
CGD / Cacao Genome Database
Provides access to sequence and annotations from the Theobroma cacao cv. Matina 1-6 cacao genome sequencing project. CGD is a comprehensive data mining resource that also provides access to several genomic tools.
CRC / Chlamydomonas Resource Center
Gathers and gives access to type and mutant cultures of Chlamydomonas reinhardtii. CRC is a repository that also provides molecular reagents and kits for educational and research purposes.
E.coli Database Portal
Provides access to several databases about Escherichia coli. E.coli Database Portal provides direct access to databases wabsites, aswell as a short description for each resource. The databases available concern (i) E.colistrain K12, (ii) pathogenic E.colistrains, and other strains.
Gathers the proteomes, organized into gene families, of several metazoans.
OXGRID / The Oxford Grid Project
Provides access to zoomable and annotated web-based Oxford grids. OXGRID is a database allowing users to browse comparative mapping data. The multiple cells view contains a grid of cells representing pairwise comparisons for each of the possible linkage group combinations and provides an overview of the comparative map. A mouse click over a selected cell launches a detailed view. The OxfordGrid software for generating an interactive Oxford grid is downloadable on the website.
HUGE / Human Unidentified Gene-Encoded
Stores results from sequence analysis of human novel large complementary DNA (cDNAs) obtained in the context of the Kazusa cDNA sequencing Project. HUGE is a database than contains more than 2000 entries. Each entry is designated “KIAA” plus a four-digit number and has its own gene/protein characteristic table, in which the results from computer-assisted analysis of the cDNA sequence and the deduced amino acid sequences are summarized.
Gathers information about bacterial and archaeal glycoproteins. ProGlycProt is a repository of published information and provides enough experimental information in the relationship between a glycoprotein, its oligosaccharyl/glycosyl transferases (OSTs/GTs), protein glycosylation-linked gene(s) and their genomic context. This database supplies an estimation of the extent of occurrence of protein glycosylation in prokaryotes.
ProtChemSI / protein-chemical structural interactions
Gathers information and data about protein-chemical topic. ProtChemSI is a resource that contains known structures of protein–chemical complexes and several other predicted complexes. The web interface of this resource offers user two possibilities: browsing the database, or searching by protein name, UniProt ID, protein sequence, ligand name, PubChem ID or SMILES string.
PROTCOM / Protein Complexes
Supplies user a set of functionalities allowing search, browse, visualization, and download of protein complexes. PROTCOM is a database that serves as a pool of templates for threading and homology modeling methods. The implementation of this database consists of two parts: two-chain protein–protein complexes and two-domain single-chain proteins.
ProtClustDB / Protein Clusters Database
Provides several information about proteins. ProtClustDB is a resource composed of two functions: (1) update RefSeq genomes with curated gene and protein information; (2) provide a central aggregation source for information collected from a wide variety of sources that would be useful for scientists studying protein-level or genomic-level molecular functions. Information contained in this database is stored in four sets or groups: prokaryotes, phages, chloroplasts and mitochondria.
Gathers information to assist scientists in research of pseudogene annotation. Pseudogene is a searchable repository for all protein-coding derived pseudogenes identified in the literature. This platform contains the following features: (1) integration of different identification methodologies; (2) flexible search capacity; (3) pre-computed search sets; (4) robust interaction with other databases; (5) temporal reconstruct-ability; and (6) simplified accessibility.
PSI SGKB / Protein Structure Initiative Structural Genomics Knowledgebase
Provides results of the protein structure initiative (PSI). PSI SGKB is a knowledge base that supplies access to the annotated protein structures, associated functional predictions, experimental protocols and tracking information and more. This resource integrates structural information with relevant scientific information from external data resources. Moreover, it informs user about a vast array of technologies, protein production protocols and software applications.
PSI-MR / Protein Structure Initiative Material Repository
Provides centralized storage and distribution for the protein expression plasmids created by PSI researchers. PSI-MR is a resource that informs about plasmids, theses plasmids permits researchers to find the biological function of protein. For each PSI plasmid, user can retrieve additional resources simplifying cross-referencing of a particular plasmid to protein annotations and experimental data.
PTGL / Protein Topology Graph Library
Allows users to retrieve and search specific protein topologies. PTGL provides searching facilities using sequence similarity in proteins. It is useful for theoretical protein structure analysis, protein structure prediction and protein function prediction. This platform provides a batch query form that accepts lists of proteins and a sequence search based on local BLAST.
PubDNA Finder
Allows user to realize advanced researches about sequences of nucleic acids. PubDNA Finder is an online repository linking PubMed Central manuscripts to the different genetic sequences appearing in them. It extends the search capabilities provided by PubMed Central by allowing researchers to: (1) retrieve all articles containing the genetic sequences specified by the user; (2) retrieve all the sequences appearing in the manuscripts matching a keyword-based query; and (3) find all articles matching a keyword-based query and containing the sequences specified by user.
QlicRice / QTL and Loci Interaction Channels in Rice
Captures and integrates genomic information on quantitative trait loci (QTLs) related to abiotic stresses in rice. QlicRice provides a query interface designed for searching genes underlying QTLs related to abiotic stresses. Its interface contains several options such as: (1) search by typing abiotic stress trait; (2) mine QTL details by submitting QTL Accession ID; and (3) query by gene locus ID.
Provides information for realizing Next-Generation Sequencing (NGS) analyses. R-Syst is a national network and informs about molecular biology, genetics and bioinformatics.
RatMap / rat genome information
Provides information about rat genome. RatMap supplies data on rat idiograms, karyotypes and presents rat genome sequence. It also integrates rat linkage maps. This resource offers user a list of tools simplifying characterization and identification of rat quantitative trait loci (QTLs).
RBCC / Red Blood Cell Collection
Assists user for identification of membrane protein. RBCC is an interactive database for detection of red blood cell (RBC) proteins from mass-spectrometry (MS) data sources. This database integrates data from several resources.
Reactome BioMart
Allows user to explore post-translational modification (PTM) details for a protein. Reactome Biomart is an online resource that can retrieve and integrate protein phosphorylation data. It gathers information about: cellular compartment of the protein; the name of the modification; the modified residue; the coordinate of the modified residue on protein sequence; and the start and stop positions of protein sequence.
Informs user about genes known to utilize translational recoding. Recode permits user to visualize annotated sequence elements, do complex search queries, and browse recoding data.
RefPrimeCouch / A Reference Gene Primer CouchApp
Allows user to find information about gene. RefPrimeCouch assists user in development of quantitative real-time polymerase chain reaction (qPCR) standardization project. This resource includes storage function and permits searching human reference genes for different tissues.
RefProtDom / a protein database with improved domain boundaries and homology relationships
Informs about relationships and alignment boundaries between query domains and target library homologs. RefProtDom uses diverse set of full-length, multi-domain, proteins in the target library. It also can simulate searches against comprehensive sequence databases while evaluating success on challenging homologies.
RegaDB / Rega database
Allows management of Human Immunodeficiency Virus (HIV) treatment, monitoring and resistance data. RegaDB is a database designed to facilitate individual patient management and also to enable real-time surveillance and research. This resource can be used to produce genotypic resistance reports. Moreover, all data reachable are anonymized.
OligoGenome / Stanford Human Oligo Genome Project
Provides oligonucleotide capture sequences that span the human genome. OligoGenome offers functions to browse, filter and download capture oligonucleotide sequences based upon user queried genomic regions and annotation-based constraints. It allows users to build query both inside and outside of the coding regions of human genome. The database can be used as a useful resource for other selective circularization technologies.
Provides exhaustive annotation and analysis of expressed sequence tag (EST) sequences in a comparative context. openSputnik is a platform on which the intricate patterns of generalist house-keeping genes and lineage-specific gene families may be teased apart. The database offers routes to the underlying data will be displayed. It allows calculation in a distributed and heterogeneous computational environment.
PA-GOSUB / Proteome Analyst: Gene Ontology molecular function and Subcellular Localization
Provides gene ontology (GO) and subcellular localization annotations. PA-GOSUB offers search and browsing capabilities that add query functionality to the pre-computed model organisms. It contains more than 140 000 proteins, about 27 000 Gene Ontology Annotation (GOA) and more than 100 000 Proteome Analyst (PA) for Gene Ontology (GO) molecular function. The database can be used to assist users to understand why a classifier makes a particular classification thank to the implementation of an explanation mechanism.
PairsDB / Pairs Database
Offers a way to facilitate the establishment of family relationships between all known protein sequences. PairsDB aims to assign functions to novel proteins and to identify conserved parts in the protein sequences. It allows exploration of protein sequences and their similarity relationships. The database is able to report distant neighbours and display query-anchored stacked alignments. It can be useful for determination of orthologous genes in completely sequenced genomes.
PANDIT / Protein and Associated Nucleotide Domains with Inferred Trees
Assists researchers to investigate molecular evolutionary phenomena and to develop phylogenetic and comparative genomic methodology. PANDIT provides a set of aligned protein coding sequences, both at the DNA and amino acid level. It offers estimation of the evolutionary trees describing the relationship between these sequences. The database allows users to quickly and efficiently produce datasets relevant for their needs.
PASS2 / Protein Alignments organised as Structural Superfamilies
Provides structure-based sequence alignments of protein domain superfamilies in correspondence with Structural Classification of Proteins (SCOP) definitions. PASS2 deals with distantly related members that diversify into multiple Pfam (Protein families) families which include more closely related and reliable set of homologues. The database has a conscious inclusion of single-member superfamilies.
Provides information on over 190 published online cellular pathway and network databases. Pathguide is organised around approximate categories and a database can be stored in multiple categories if it contains multiple data types. The main categories for databases are: Protein–protein interaction (PPI), Metabolic pathway, Signaling pathway, Gene regulation network (GRN), Genetic pathway and Pathway diagram. The database includes a number of protein-sequence databases that store pathway information as secondary information.
Provides annotated protein functional sites. PDBSite integrates physicochemical, structural and functional characteristics of the sites. It was used to search novel functional sites in the mutants of the DNA-binding domain of human protein p53 resulting from tumor-associated mutations. The database allows comparison of target protein against known functional sites. It offers a flexible search for proteins on the basis of description of their functional sites.
Captures and stores peptide identification information. PepSeeker allows users to query it to help mine rules and explore fragmentation patterns observed in peptide sequences studied in the mass spectrometer. It contains both peptide identifications and associated fragment ion details used to identify amino acid sequence. The database aims to provide datasets for groups developing tools for peptide identification.
Provides a high-quality mass spectra repository. Peptidome aims to enhance proteomic research. It offers user-friendly tools that enable users to query, locate, analyze and review the data of interest. The database makes data submission procedures as straightforward as possible, while encouraging a high level of experimental annotation. It accepts native file formats from which required information is extracted.
PepX / Protein-peptide complexes
Provides information about protein-peptide complexes available in the Protein Data Bank (PDB). PepX concerns protein-peptide complexes with peptide lengths up to 35 residues. It provides an additional service for peptide design thank to the exploitation of the scarcity of protein–peptide structures and their obvious relevance in drug design. The database associates ligand peptides with its corresponding structural class from the database of protein fragment classes.
Offers a global overview on peroxidases. PeroxiBase centralizes data concerning class III peroxidases from Viridiplantae. It offers a multicriteria tool that allows several methods for refining and limiting a query as well as combining several queries. The database permits evolutionary analysis thanks to the availability of a package of tools. It can be useful for researchers who need to make complex phylogenetic analysis.
PFD / Protein Folding Database
Provides data about protein folding. PFD provides annotated information, enriched with experimental, structural and functional details. It is searchable using many parameters, as well as retrieval and presentation of data. The database can be used to the biophysicist seeking to compare new folding data with the current dataset for similar proteins. It can be useful for designing folding experiments.
PFGD / Phytophthora Functional Genomics Database
Captures heterogeneous data about gene and protein sequences, gene expression patterns, biological activity, as well as cellular responses and localization during infection in a useful and intuitive way for biological researchers. PFGD allows users to access and compare data via a multifaceted web interface. It supports curation and visualization of functional assay experiments.
PGD / Pangolin Genome Database
Provides resources and information of pangolins, together with useful analysis tools for the research community. PGD permits users to search, browse, retrieve, visualize and analyze pangolin genomic and transcriptomic data and information. It stores the sequences of expressed genes from different organs, namely the cerebellum, cerebrum, liver, heart, kidney, lung, thymus and spleen of the Malayan pangolin.
PGD / Protein Geometry Database
Allows exploration of peptide geometry, peptide conformation, and the ties between them. PGD contains derived data for a complete, representative data set of protein structures that are relevant to discovering reliable instances of conformations and peptide geometries. It contains data on per-chain and per-residue levels. The database stores parameters including the Protein Data Bank (PDB) code, the chain ID, the sequence-identity threshold, the resolution, and the crystallographic R-factor.
PharmGED / Pharmacogenetic Effect Database
Provides information about the effects of a particular protein polymorphism, non-coding region mutation, splicing alteration or expression variation on the response of a particular drug. PharmGED contains more than 1800 entries covering 100 disease conditions, 250 distinct proteins, about 700 polymorphisms, and 400 drugs/ligands. It aims to facilitate pharmacogenetic study and can be useful to predict various types of individual variations of drug responses.
LccED / The Laccase Engineering Database
Enables the systematic classification and analysis of multicopper oxidases (MCO) sequences and structures from different public sources. LccED combines information on sequences, sequence alignments, annotations, and structures of MCOs. The database contains data about more than 2000 sequences and 200 proteins. Users can browse the data by family, organism or structure. A set of tools for phylogenetic analysis and classification is also available.
LEAPdb / Late Embryogenesis Abundant Proteins database
Harbors a comprehensive data set for late embryogenesis abundant proteins (LEAP) with tools designed for their online analysis. LEAPdb provides a curated archive of LEAP families to navigate, interpret, and understand this data. The database includes functions to search, describe and analyze LEAP. It can be useful for the compilation and the organization of data concerning LEAP, the classification of the various sub-families, the design of experiments to elucidate the function of this proteins and to help the analysis of the LEAP structure-function relationships.
Provides information about length-variant protein domains. LenVarDB systematically and automatically gathers sequences, aligns them to pre-existing structure-guided Protein Alignments organized as Structural Superfamilies (PASS2) alignments and derives indel (length-variant)- prone regions of protein domain superfamilies. The database allows users to identify the indel-prone regions, which can enable rational design of bioengineering experiments.
Provides integrated access to complementary DNA (cDNA)-data, experimental results and bioinformatics information. LIFEdb is a database enabling researchers to systematically select and characterize genes and proteins of interest. The database was developed to publish data on full-length cDNAs and the subcellular localization of the encoded proteins.
Provides information about lipid-related Gene Ontology (GO) terms and gene products. LipidGO is a platform that allows users to search by key words to obtain the list of GO terms and by GO accession number that gives detailed information about the term and its related gene products. Users can download the GO subtree rooted at a term and see which branches are lipid related.
LMPD / Lipid Maps Proteome Database
Provides access to lipid-associated protein sequences and annotations. LMPD is a database that stores more than 8.000 genes and 12.000 proteins from several species, including human. Users can browse the protein list, with an option to browse by associated lipid category. The ‘Advanced’ query form includes options to search by database ID or keyword and to filter by species and/or lipid class association.
LMSD / Lipid Maps Structure Database
Gathers structures and annotations of biologically relevant lipids. LMSD is a database of lipids that has several features: (i) usage of hierarchical classification and consistent nomenclature based on a comprehensive classification scheme proposed by LIPID MAPS, (ii) a unique LIPID MAPS identifier (LM ID) assignment to all structures, (iii) no duplicate structures and, (iv) ability to search database using structure.
LPSN / List of Prokaryotic Names with Standing in Nomenclature
Gathers the names of prokaryotes (Bacteria and Archaea) published in the International Journal of Systematic and Evolutionary Microbiology (IJSEM) directly or by inclusion in a Validation List, under the Rules of International Code of Nomenclature of Bacteria. LPSN provides information about the current status of a name and its synonyms. The classification is based on (i) the original publications, and/or the latest “Taxonomic Outline of the Bacteria and Archaea”, (ii) and/or the “NCBI Taxonomy Browser” and/or (iii) “The All-Species Living Tree Project”.
Integrates disparate data sets related to ancient life. LUCapedia is designed for users interested in quickly collecting evidence of deep ancestry for a small number of protein families. Users can query the database for a single protein to collect evidence of its antiquity from a broad range of studies. The database allows to corroborate the results from independent studies, to evaluate early life hypotheses, and to direct future experiments towards understudied areas.
MDM-Portal / Medical Data Models- Portal
Facilitates sharing of medical data models. MDM-Portal is a registered German and European information infrastructure that provides a multilingual platform for exchange and discussion of data models in medicine, both for medical research and healthcare. The database contains more than 4000 data models. Most contents of the MDM portal were derived from clinical trials and each data model can be tagged with one or several keywords from the MeSH thesaurus.
Gathers structural segments or motifs for protein structures. MegaMotifbase provides a compilation of structural motifs identified through a completely automated method for large number of families and superfamilies of proteins. Motifs contained in the database can assist in the identification of new potential members of an existing family and/or superfamily. MegaMotifbase provides the application of sequence–structural templates in three different areas: multimotif-based sequence search, multiple sequence alignment and homology modeling.
MB / MetaBase
Lists more than 2000 commonly used biological databases. MetaBase (MB) is a wiki-based database of biological databases. Users can search, query or browse the data by category and can also contribute, update and maintain the data. Each database in MB is described in a semi-structured way using forms and templates. Entries carry data for various fields and allow a free-text description of the resource.
Gathers evidences and hypotheses that are relevant to the improvement of the culture conditions of obligate parasites. Metagrowth is a knowledgebase with a web interface guiding the user to design new cell-free culture media of obligate parasites. The database contains more than 200 entries for 6 species of bacteria (5 genera). It aims to assist the scientific community working on those pathogens by providing comprehensive information about their culture conditions.
MetaMetaDB / Meta- Metagenomic Data Base
Collects 16S rRNA sequences from a large number of datasets. MetaMetaDB is a comprehensive (‘‘meta-’’) and compact database that contains collection of 16S rRNA sequences associated with diverse environments. Users can submit the 16S rRNA sequences of certain prokaryotes and thus can investigate the microbial habitability for analyzing the ecology and evolution of prokaryotes. The database provides a reverse perspective of the environments in which each prokaryotic group exists, opening the door to the investigation of ‘‘meta-metagenomics’’.
Maintains heterogeneous information related to bioremediation and biodegradation. MetaRouter is a relational database where the information on chemical compounds, reactions, enzymes and organisms is stored in an integrated framework. Users can consult the database and formulate new questions with associated programs that run on top of the database. MetaRouter can assist researchers in assessing the environmental fate of compounds or mixtures and in designing biodegradative strategies for them.
METscout / Metabolites Enzymes and Transporters scout
Gathers metabolic pathway maps with the expression patterns of about 1500 metabolic enzyme genes and 350 metabolite transporter genes. METscout is a gene-centric database with an almost full coverage of metabolic network components of mouse, based on expression data for the E14.5 mouse embryo. The database allows users to explore the spatial organization of metabolic pathways and metabolite transport in the whole organism. It also provides a basic framework to investigate whether and how pathways may change under pathological conditions.
MGEx-Udb / Mammalian Gene Expression Uterus database
Compiles uterine gene expression data from studies on human, mouse, rat, cow and pig species. MGEx-Udb can be queried by gene, user or identifiers (names, symbols, synonyms, Entrez gene IDs, and gene keywords/descriptions). The database provides most or all of the genes associated with a specific condition, and thus can serve as a starting point for any kind of functional analysis for various uterine conditions. It also provides an opportunity to compare gene expression patterns across subtle variations in conditions and treatments.
MisPred / Miss Predict Protein Database
Allows to identify erroneous (abnormal, incomplete and mispredicted) protein sequences in public databases. MisPred is a database that contains more than 80800 erroneous sequences identified in 19 metazoan species. It provides for each entry the protein ID, the protein description, the database source, the species name and the type of sequence error(s) identified. Users can also analyse protein sequences for possible sequence errors using the MisPred quality control tools.
VGNC / Vertebrate Gene Nomenclature Committee
Supplies several information about vertebrate species. VGNC is an online platform that shares consistent branding with the HUGO Gene Nomenclature Committee (HGNC) site and replicates some of the displays provided for the HGNC data. Each webpage of this resource has a header containing links that enable browsing of various sections of the website. A footer provides a site map, allowing user to jump to a specific page of interest.
WDCM / World Data Centre for Microorganisms
Serves as an information resource for the customers of the microbial resource centers. WDCM was launched in 1966 and contains currently the global registry for culture collections to serve as an informatics resource for the user community.
Xanthusbase / Myxococcus xanthus databse
Gathers information about the bacterium Myxococcus xanthus. Xanthusbase is an educational database that informs about genome annotation. This tool is a variable alternative curation schema that will enable smaller research communities to support the official model organism database (MOD).
YH / YanHuang
Simplifies study of the Asian genome. YH is an online resource where YanHuang genome and the processed variations are saved in standard format in order to enable data sharing and transformation. This database also provides suitable utilities for analyses, and one of its purpose is to analyze personal genome data.
YRC PIR / The Yeast Resource Center Public Image Repository
Provides a large number of images and their associated metadata for many proteins across multiple organisms. YRC PIR is a database of fluorescence microscopy images. It allows researchers to find, view, and download many images and associated metadata depicting the subcellular localization and co-localization of proteins.
ThYme / Thioester-active enzYme
Finds naturally occurring enzymes. ThYme presents enzymes acting on thioester-containing substrates, especially those involved in fatty acid and polyketide synthesis. This online resource also facilitates enzyme design and encompasses eight enzyme groups. It also helps to predict active sites, catalytic residues and mechanisms of individual sequences, as well as providing a standardized nomenclature.
TMAD / Stanford Tissue MicroArray Database
Provides tools to assist the histologist with array block design and construction. TMAD is an online resource that equips researchers with tissue microarray design tools, image scoring and annotation tools, data sharing mechanisms, an image archive, an analysis toolset and publication mechanism. It also offers a graphical browser to the full ontology with clickable links for browsing to more general or specific terms.
Provides annotated b-barrel membrane proteins for completed genomes. TMBETA-GENOME includes several features, such as the service for detecting transmembrane b-barrel proteins (TMBs) in genomic sequences using various methods, related references, statistics for the detected TMBs by different methods for each genome, details about all algorithms used to detect TMBs, relative links to other databases and a help page.
tmBioC / text-mining BioC
Provides a BioC version of a suite. tmBioC is an annotated full-text corpus in BioC, a format detection and a conversion tool.
Helps in understanding the relationship between amino acid sequences/structures and functions of membrane proteins. TMFunction is a collection of more than 2900 experimental data about important amino acid residues in membrane proteins, reported in the literature. This resource includes features to: (i) retrieve data for a particular protein and/or source, (ii) specify the type of the mutant as single, multiple and/or wild-type, (iii) select the function of the protein, (iv) mention the type of the protein, (v) extract data by authors, publication year and keywords, and (vi) download entire data.
tomatEST / Tomato Expressed Sequence Tag
Supports investigations on expressed sequence data from multiple tomato species. tomatEST is a database of expressed sequence tag (EST) /complementary DNA (cDNA) sequences from dbEST libraries, a division of GenBank containing sequence data. This resource was developed to provide a workbench for mining the complexity of EST sequence information content from multiple tomato species (i) for expression pattern analysis and (ii) for gene discovery in the framework of Solanum lycopersicum genome project.
The Online Protein Processing Resource / TOPPR
Provides a platform for discovery and analysis to both protease researchers and scientists studying a single substrate. TOPPR is a resource that contains published proteolytically processed sites in proteins of human and mouse. This resource also serves as a powerful exploration platform to verify data quality, assess protease specificity, perform processing site motif analyses and carry out detailed substrate analyses.
TparvaDB / Theileria parva vaccine development Database
Provides a unified platform for all genome and related Theileria parva data. TparvaDB is a comprehensive resource to facilitate research in the development of an East Coast fever (ECF) vaccine and comparative Apicomplexan genomics. This resource was built using components of the Generic Model Organism Database system. It contains complete reference genome sequence, Expressed Sequence Tags (ESTs), Massively Parallel Signature Sequencing (MPSS) expression tag data and related information from both public and private repositories.
TPMD / Taiwan Polymorphic Marker Database
Offers experimental details and marker information allelotyped in population of Taiwan. TPMD is a shared database and resources for genotyping with microsatellite markers that reduces cost and errors of genotyping and facilitates disease gene mapping in human populations. This resource contains two major sections including the database for sharing useful microsatellite marker information and the resources for supporting consistent genotyping experiments.
Detects mutual drug impairments and helps to appraise the drug response. Transformer is a comprehensive resource that combines scientific information on phase I and phase II reactions of enzymes, transporter enzymes, prodrugs, food and herbs that increase risk of adverse drug reactions. This resource can be a sound starting point for further research in drug interactions.
TSLP signaling pathway map / Thymic stromal lymphopoietin signaling pathway map
Provides signal transduction pathways in humans. TSLP signaling pathway map is a manually curated resource made with PathVisio, a pathway drawing software. This map resource provides a map that includes about 236 molecules and 252 reactions involved in Thymic stromal lymphopoietin (TSLP) and TSLP receptor (TSLPR) signaling pathway. It also aids in understanding the role of various molecules in biology.