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NAR Database Issue 2011

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3didDatabase Content

http://3did.irbbarcelona.org/ [open in a new window]

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Protein > 3-D Structure Retrieval/Viewing
Protein > Databases

The database of three-dimensional interacting domains (3did) is a collection of protein interactions for which high-resolution three-dimensional structures are known. The interface residues are presented for each interaction type individually, plus global domain interfaces at which one or more partners (domains or peptides) bind. The 3did web server visualizes these interfaces along with atomic details of individual interactions using Jmol.

links directory index: 21
TitlePublication YearGoogle Scholar Citation Count
3did: identification and classification of domain-based interactions of known three-dimensional structure201121
NAR Database Issue 2011
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tagsmolecular models peptides protein databases protein interaction domains and motifs protein interaction mapping

AgBaseDatabase Content

http://www.agbase.msstate.edu/ [open in a new window]

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Model Organisms > Databases

AgBase provides resources to facilitate modeling of functional genomics data and structural and functional annotation of agriculturally important animal, plant, microbe and parasite genomes. One of seven new tools available at AgBase, GOModeler, supports hypothesis testing from functional genomics data. Moreover, we provide comprehensive training resources (including worked examples and tutorials) via links to Educational Resources at the AgBase website.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
AgBase: supporting functional modeling in agricultural organisms20116
NAR Database Issue 2011
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tagsagricultural crops agriculture animals cats dogs domestic animals gene expression profiling genetic databases genetic models genomics oligonucleotide array sequence analysis

AGRISDatabase Content

http://arabidopsis.med.ohio-state.edu/ [open in a new window]

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Model Organisms > Databases

The Arabidopsis Gene Regulatory Information Server (AGRIS) provides a comprehensive resource for gene regulatory studies in the model plant Arabidopsis thaliana. Three interlinked databases, AtTFDB, AtcisDB and AtRegNet, furnish comprehensive and updated information on transcription factors (TFs), predicted and experimentally verified cis-regulatory elements (CREs) and their interactions, respectively.

links directory index: 19
TitlePublication YearGoogle Scholar Citation Count
AGRIS: the Arabidopsis Gene Regulatory Information Server, an update201119
NAR Database Issue 2011
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tagsarabidopsis gene regulatory networks genetic databases genetic promoter regions plant gene expression regulation transcription factors

AHD2.0Database Content

http://ahd.cbi.pku.edu.cn/ [open in a new window]

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Model Organisms > Databases

Arabidopsis Hormone Database (AHD) is a collection of hormone related genes of the model organism Arabidopsis thaliana (AHRGs). AHD2.0 has new features: (i) updating our collection of AHRGs based on most recent publications as well as constructing elaborate schematic diagrams of each hormone biosynthesis and signaling pathways; (ii) adding orthologs of sequenced plants listed in OrthoMCL-DB to each AHRG in the updated database; (iii) providing predicted miRNA splicing site(s) for each AHRG; (iv) integrating genes that genetically interact with each AHRG according to literatures mining; (v) providing links to a powerful online analysis platform WebLab for the convenience of in-time bioinformatics analysis and (vi) providing links to widely used protein databases and integrating more expression profiling information that would facilitate users for a more systematic and integrative analysis related to phytohormone research.

links directory index: 2
TitlePublication YearGoogle Scholar Citation Count
AHD2.0: an update version of Arabidopsis Hormone Database for plant systematic studies20112
NAR Database Issue 2011
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tagsarabidopsis genetic databases micrornas plant genes plant growth regulators rna splicing

Allele frequency netDatabase Content

http://www.allelefrequencies.net [open in a new window]

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Human Genome > Databases

The allele frequency net database is an online repository that contains information on the frequencies of immune genes and their corresponding alleles in different populations. At present, the system contains data on the frequency of genes from different polymorphic regions such as human leukocyte antigens, killer-cell immunoglobulin-like receptors, major histocompatibility complex Class I chain-related genes and a number of cytokine gene polymorphisms.

links directory index: 58
TitlePublication YearGoogle Scholar Citation Count
Allele frequency net: a database and online repository for immune gene frequencies in worldwide populations201158
NAR Database Issue 2011
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tagscytokines gene frequency genotype haplotypes histocompatibility antigens class i humans kir receptors major histocompatibility complex nucleic acid databases

AmoebaDB and MicrosporidiaDBDatabase Content

http://AmoebaDB.org [open in a new window]

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Model Organisms > Databases

AmoebaDB and MicrosporidiaDB are functional genomic databases serving the amoebozoa and microsporidia research communities, respectively. AmoebaDB contains the genomes of three Entamoeba species (E. dispar, E. invadens and E. histolityca) and microarray expression data for E. histolytica. MicrosporidiaDB contains the genomes of Encephalitozoon cuniculi, E. intestinalis and E. bieneusi. Genomic scale data can be queried based on BLAST searches, annotation keywords and gene ID searches, GO terms, sequence motifs, protein characteristics, phylogenetic relationships and functional data such as transcript (microarray and EST evidence) and protein expression data. Search strategies can be saved within a user's profile for future retrieval and may also be shared with other researchers using a unique strategy web address.

links directory index: 8
TitlePublication YearGoogle Scholar Citation Count
AmoebaDB and MicrosporidiaDB: functional genomic resources for Amoebozoa and Microsporidia species20118
NAR Database Issue 2011
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tagsencephalitozoon entamoeba fungal genome genetic databases genomics protozoan genome

ArachnoServer 2.0Database Content

http://www.arachnoserver.org [open in a new window]

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Model Organisms > Databases
Protein > Databases

ArachnoServer is a manually curated database providing information on the sequence, structure and biological activity of protein toxins from spider venoms. Key features of ArachnoServer include a molecular target ontology designed specifically for venom toxins, current and historic taxonomic information and a powerful advanced search interface.

This content is being maintained by glennfking.

links directory index: 29
TitlePublication YearGoogle Scholar Citation Count
ArachnoServer 2.0, an updated online resource for spider toxin sequences and structures201113
ArachnoServer: a database of protein toxins from spiders200916
NAR Database Issue 2011
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tagsanimals protein databases proteins sequence analysis spider venoms spiders

AREsiteDatabase Content

http://rna.tbi.univie.ac.at/AREsite [open in a new window]

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RNA > Databases

AREsite is an online resource for the detailed investigation of AU-rich elements (ARE) in vertebrate mRNA 3'-untranslated regions (UTRs). AREsite allows one to quantify the structuredness of ARE motif sites in terms of opening energies and accessibility probabilities. A detailed phylogenetic analysis of ARE motifs and incorporate information about experimentally validated targets of the ARE-binding proteins TTP, HuR and Auf1 is also provided.

links directory index: 13
TitlePublication YearGoogle Scholar Citation Count
AREsite: a database for the comprehensive investigation of AU-rich elements201113
NAR Database Issue 2011
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tags3' untranslated regions adenine animals base sequence conserved sequence genomics humans mice nucleic acid databases rna sequence analysis rna-binding proteins sequence alignment uracil

ArrayExpress updateDatabase Content

http://www.ebi.ac.uk/arrayexpress [open in a new window]

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Expression > Databases

The ArrayExpress Archive is a public repository of functional genomics data supporting publications. It includes data generated by sequencing or array-based technologies. Data are submitted by users and imported directly from the NCBI Gene Expression Omnibus. The ArrayExpress Archive is closely integrated with the Gene Expression Atlas and the sequence databases at the European Bioinformatics Institute. Advanced queries provided via ontology enabled interfaces include queries based on technology and sample attributes such as disease, cell types and anatomy.

links directory index: 60
TitlePublication YearGoogle Scholar Citation Count
ArrayExpress update--an archive of microarray and high-throughput sequencing-based functional genomics experiments201160
NAR Database Issue 2011
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tagsgene expression gene expression profiling genetic databases genomics high-throughput nucleotide sequencing oligonucleotide array sequence analysis

ASDDatabase Content

http://mdl.shsmu.edu.cn/ASD/ [open in a new window]

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Protein > Databases

AlloSteric Database (ASD) provides a central resource for the display, search and analysis of structure, function and related annotation for allosteric molecules. Proteins are annotated with a detailed description of allostery, biological process and related diseases, and modulators with binding affinity, physicochemical properties and therapeutic area.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
ASD: a comprehensive database of allosteric proteins and modulators20114
NAR Database Issue 2011
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tagsallosteric regulation allosteric site drug design protein databases proteins

ASPicDBDatabase Content

http://www.caspur.it/ASPicDB/ [open in a new window]

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Human Genome > Databases
Protein > Databases

ASPicDB provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256,939 protein variants from 17,191 multi-exon genes have been extensively annotated through machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user.

This content is being maintained by Graziano Pesole.

links directory index: 3
TitlePublication YearGoogle Scholar Citation Count
ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing20113
NAR Database Issue 2011
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tagsalternative splicing exons genetic databases genetic variation humans messenger rna protein isoforms protein sequence analysis proteins

AtPIDDatabase Content

http://www.megabionet.org/atpid/ [open in a new window]

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Model Organisms > Databases
Protein > Databases

The AtPID (Arabidopsis thaliana Protein Interactome Database) represents a centralized platform to depict and integrate the information pertaining to protein-protein interaction networks, domain architecture, ortholog information and GO annotation in the Arabidopsis thaliana proteome.

links directory index: 4
TitlePublication YearGoogle Scholar Citation Count
AtPID: the overall hierarchical functional protein interaction network interface and analytic platform for Arabidopsis20114
NAR Database Issue 2011
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tagsarabidopsis proteins molecular sequence annotation protein databases protein interaction mapping proteomics

BioDBcoreDatabase Content

http://biocurator.org/biodbcore.shtml [open in a new window]

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BioDBCore is a community-defined, uniform, generic description of the core attributes of biological databases.

This content is being maintained by pgaudet.

links directory index: 17
TitlePublication YearGoogle Scholar Citation Count
Towards BioDBcore: a community-defined information specification for biological databases201117
NAR Database Issue 2011
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tagsfactual databases information dissemination

BISCDatabase Content

http://bisc.cse.ucsc.edu [open in a new window]

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Protein > Databases

Binary subcomplexes in proteins database (BISC) is a protein-protein interaction (PPI) database linking up the two communities most active in their characterization: structural biology and functional genomics researchers. The BISC resource offers users (i) a structural perspective and related information about binary subcomplexes (i.e. physical direct interactions between proteins) that are either structurally characterized or modellable entries in the main functional genomics PPI databases BioGRID, IntAct and HPRD; (ii) selected web services to further investigate the validity of postulated PPI by inspection of their hypothetical modelled interfaces.

links directory index: 1
TitlePublication YearGoogle Scholar Citation Count
BISC: binary subcomplexes in proteins database20111
NAR Database Issue 2011
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external linksLink on Wikipedia
tagsgenetic databases genomics molecular models multiprotein complexes protein databases protein interaction mapping

Bovine Genome DatabaseDatabase Content

http://BovineGenome.org [open in a new window]

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Model Organisms > Databases

The Bovine Genome Database (BGD) includes mechanisms too improve annotation of the bovine genome and to integrate the genome sequence with other genomics data. BGD includes GBrowse genome browsers, the Apollo Annotation Editor, a quantitative trait loci (QTL) viewer, BLAST databases and gene pages. Genome browsers, available for both scaffold and chromosome coordinate systems, display the bovine Official Gene Set (OGS), RefSeq and Ensembl gene models, non-coding RNA, repeats, pseudogenes, single-nucleotide polymorphism, markers, QTL and alignments to complementary DNAs, ESTs and protein homologs. Researchers may upload their annotations to the BGD server for review and integration into the subsequent release of the OGS.

links directory index: 6
TitlePublication YearGoogle Scholar Citation Count
Bovine Genome Database: integrated tools for genome annotation and discovery20116
NAR Database Issue 2011
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tagsanimals cattle genetic databases genetic models genome genomics molecular sequence annotation quantitative trait loci sequence alignment systems integration

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