bioinformatics-databases

Integrative and conjugative elements (ICEs) are a diverse group of mobile genetic elements found in both Gram-positive and Gram-negative bacteria. ICEs are self-transmissible elements that encode a full complement of machinery for conjugation as well as intricate regulatory systems to control excision from the chromosome and onward conjugative transfer [Wozniak and Waldor, 2010; Burrus,2004]. These multi-talented entities can promote their own mobilization and potentially that of other 'hitch-hiking' genetic elements and thus contribute to horizontal transfer of virulence determinants, antibiotic-resistance genes and other bacterial traits [Hastings. et al., 2004]. 

ICEs are being identified in increasing numbers as sequenced genome databases expand exponentially [Wozniak, et al., 2010; Ryan, et al., 2009; te Poele, et al., 2008; Burrus et al., 2002]. At present only a few have been classified into ICE families, amongst the best characterized of which is the SXT/R391 family of Vibrio cholerae, like  SXT of Vibrio choleraeO139 MO10. In addition, several elements discovered more than a decade ago which had previously been classified as plasmids or conjugative transposons, such as  pSAM2 and Tn916 , have now been defined as ICEs. ICEs typically exhibit a number of features that are of interest to researchers in the fields of prokaryotic evolution, pathogenesis, biotechnology and metabolism. These include high levels of functional diversity, foreign and frequently patchwork origins and sparse experimental data on these entities. 

We are collating available experimental and bioinformatics analyses data and literature about known and putative ICEs in bacteria as a PostgreSQL-based database called ICEberg. As its name implies we expect that ICEberg will continue to grow from its currently visible tiny 'tip' representing presently known ICEs to a very substantial database as more and more of these entities are revealed. 

HaploReg is a tool for exploring annotations of the noncoding genome at variants on haplotype blocks, such as candidate regulatory SNPs at disease-associated loci. Using LD information from the 1000 Genomes Project, linked SNPs and small indels can be visualized along with their predicted chromatin state, their sequence conservation across mammals, and their effect on regulatory motifs. HaploReg is designed for researchers developing mechanistic hypotheses of the impact of non-coding variants on clinical phenotypes and normal variation.

Update 2013.02.14: Version 2 now includes an expanded library of SNPs (based on dbSNP 137), motif instances (based on PWMs discovered from ENCODE experiments), enhancer annotations (adding 90 cell types from the Roadmap Epigenome Mapping Consortium), and eQTLs (from the GTex eQTL browser). In addition, LD calculations are provided based on the 1000 Genomes Phase 1 individuals, and r² and D' measurements are available down to an r² threshold of 0.2. Display improvements include improved cell metadata, gene metadata, and PWM display on the detail pages and the option for text output.

Version 1 is available here.

The Gene Weaver database - A Functional genomics analysis system.

eQuilibrator is a simple web interface designed to enable easy thermodynamic analysis of biochemical systems. eQuilibrator enables free-text search for biochemical compounds and reactions and provides thermodynamic estimates for both in a variety of conditions.

Estimation of thermodynamic parameters (ΔrG and ΔfG) elucidates how much energy is required to drive a particular biochemical reaction and in which direction the reaction will flow in particular cellular conditions [1-2].

Because experimental measurement of the free energy of formation (ΔfG°) of compounds is technically challenging, the vast majority of known metabolites have not been thermodynamically characterized. eQuilibrator uses a well-studied approximation of ΔfG called group contribution [3-4], enabling thermodynamic analysis of many biochemical reactions and pathways.

Currently, eQuilibrator can provide estimates for many compounds in the KEGG database [5] (about 4500). Individual compounds and enzymes can be searched for by their common names ("water", "glucosamine", "hexokinase"), and reactions can be entered in a simple, free-text format ("ribulose bisphosphate + CO2 + water => 2 3-phosphoglycerate") that eQuilibrator parses automatically. eQuilibrator also allows manipulation of the conditions of a reaction - pH, ionic strength, and reactant and product concentrations - to help explore the thermodynamic landscape of a biochemical reaction.

eQuilibrator is a project of the Milo Lab at the Weizmann Institute in Rehovot, Israel. If you have any thoughts or questions feel free to write us a note at contact@equilibrator.weizmann.ac.il.

DBETH provides a platform to its users to identify potential exotoxin like sequences through Homology based as well as Non-homology based methods. In homology based approach the users can identify potential exotoxin like sequences either running BLASTp against the toxin sequences or by running HMMER against toxin domains identified by DBETH from human pathogenic bacterial exotoxins. In Non-homology based part DBETH uses a machine learning approach to identify potential exotoxins (Toxin Prediction by Support Vector Machine based approach).

Cube-DB is a database of pre-evaluated conservation and specialization scores for residues in paralogous proteins belonging to multi-member families of human proteins. Protein family classification follows (largely) the classification suggested by HUGO Gene Nomenclature Committee. Sets of orhtologousprotein sequences were generated by mutual-best-hit strategy using full vertebrate genomes available in Ensembl. The scores, described ondocumentation page, are assigned to each individual residue in a protein, and presented in the form of a table (html or downloadable xls formats) and mapped, when appropriate, onto the related structure (Jmol, Pymol, Chimera). Please check out or featured pages below, or click on "Browse" link on the right to get the full listing of available results.

Datasets at ccPDB can be classified in two categories, i) datasets collected from literature and ii) datasets compiled from PDB. These datasets were generated using commonly used standard protocols like non-redundant chains, structures solved at high resolution.

BitterDB currently holds over 550 bitter compounds obtained from the literature and from Merck index and their associated 25 human bitter taste receptors (hT2Rs).

AutismKB is an evidence-based knowledgebase of ASD genetics. The current version contains 2193 genes (99 syndromic autism related genes and 2135 non-syndromic autism related genes), 4617 Copy Number Variations (CNVs) and 158 linkage regions associated with ASD.

FeatureExtract lets you extract sequence and feature annotations, such as intron/exon structures, from GenBank entries and other GenBank format files.

 

AMUSER-1.0 MAIT_Match-1.0 NetMHC-4.0 NetStart-1.0 SignalP-5.0 ArrayPitope-1.0 MHCMotifDecon-1.0 NetMHCII-2.3 NetSurfP-1.1 SigniSite-2.1 Barracoda-1.0 MHCcluster-2.0 NetMHCIIpan-2.1 NetSurfP-2.0 TCRpMHCmodels-1.0 BepiPred-2.0 MatrixPlot-1.2 NetMHCIIpan-3.2 NetTCR TCRpMHCmodels-1.0_old BioReader-1.2 MaxAlign-1.1 NetMHCIIpan-4.0 NetTepi-1.0 TMHMM-2.0 CPHmodels-3.2 MuPeXI-1.1 NetMHCIIpan-4.1 NetTurnP-1.0 TargetP-1.1 ChloroP-1.1 NNAlign-2.0 NetMHCcons-1.1 NetUTR-1.0 TargetP-2.0 Cofactory-1.0 NNAlign-2.1 NetMHCpan-2.8 OligoWiz-1.0 TatP-1.0 DeepLoc-1.0 NetAcet-1.0 NetMHCpan-4.0 OligoWiz-2.0 ThermoP-1.0 DictyOGlyc-1.1 NetAspGene-1.0 NetMHCpan-4.1 PickPocket-1.1 TreeHugger-0.5 DiscoTope-2.0 NetCGlyc-1.0 NetMHCphosPan-1.0 ProP-1.0 TumorTracer-1.1 EasyGene-1.2 NetCTL-1.2 NetMHCstab-1.0 Promoter-2.0 VDJsolver-1.0 EasyGibbs-1.0 NetCTLpan-1.1 NetMHCstabpan-1.0 RNAmmer-1.2 VarDom-1.0 FeatureExtract-1.2 NetChop-3.1 NetNES-1.1 RedHom-1.0 VirtualPulldown-1.1b GibbsCluster-2.0 NetCorona-1.0 NetNGlyc-1.0 RevTrans-1.4 VirtualRibosome-2.0 HExpoChem-1.0 NetDiseaseSNP-1.0 NetOGlyc-4.0 RevTrans-2.0 Von-Frey HMMgene-1.1 NetGene2-2.42 NetPhos-3.1 SecretomeP-1.0 YinOYang-1.2 InterMap3D-1.3 NetGlycate-1.0 NetPhosBac-1.0 SecretomeP-2.0 distanceP-1.0 LYRA-1.0 NetH2pan-1.0 NetPhosYeast-1.0 SignalP-3.0 pHSol-1.1 LipoP-1.0 NetMHC-3.4 NetPhospan-1.0 SignalP-4.1  

Database containing oligonucleotides for targeted resequencing of the human genome.

The Hemorrhagic Fever Viruses (HFV) Database Project is funded through the Defense Department's Transformational Medical Technologies (TMT). The HFV database group strives to present HFV-associated genetic data in a userfriendly way, by providing access to the central database via web-accessible search interfaces and supplying a number of analysis tools. 

This project is deeply indebted to the HIV Database Group, led by Dr Bette Korber, for much of its tools, infrastructure and philosophy; the databases continue to collaborate closely and to share software and resources.

EMBL EPI's FunTree database is designed for the evolution of novel enzyme functions in enzyme superfamilies.

DOMMINO is a comprehensive structural database on macromolecular interaction.

DOMMINO is a comprehensive structural database on macromolecular interactions. As of June, 2011, it contains more than 407,000 binary interactions. The distinctive features of DOMMINO are:

1. Automated updates: DOMMINO is fully automated and is designed to update itself on a weekly basis, one day after a PDB weekly update. Thus, the community will be able to study macromolecular interactions almost immediately after they are released by PDB.

2. Coverage of non-domain mediated interactions: In addition to domain-domain and domain-peptide interactions the database characterizes the interaction between domains and unstructured protein regions that are not parts of a domain, such as inter-domain linkers and N- and C-termini. The interactions that involve the latter unstructured parts of proteins have been included to the database for the first time providing additional ~186,000 interactions (~45% of the total number of interactions, as of June, 2011).

3. Coverage of new structural domains: DOMMINO employs one of the most accurate structural classifications of proteins, SCOP. In addition to the existing SCOP-annotated domains, we employ a state-of-the-art machine learning approach to classify newer protein structures into existing SCOP families. With the progress of structural genomics, we do not expect a significant growth of the number of structurally novel folds or protein families and therefore our method allows covering almost all new protein structures. In total, using this predictive approach has allowed us to add more than 261,000 new interactions, almost twice as many as existing SCOP-annotated interactions.

4. The web-interface is designed to give the user a possibility of a flexible search as well as the capability to study macromolecular interactions in a PDB structure at the interaction network level and at the individual interface level.

The web interface of the DOMMINO database includes a comprehensive list of help topics linked to the specific actions. In addition, we have designed a step-by-step tutorial that covers all aspects of working with the data from DOMMINO using the web interface.

How to cite us: 
Kuang X, Han JG, Zhao N, Pang B, Shyu CR, Korkin D. "DOMMINO: A database of macromolecular interactions"; Nucleic Acids Res., (2012), 40 (database issue), D501-D506.

The human disease methylation database, DiseaseMeth is a web based resource focused on the aberrant methylomes of human diseases. Until recently, bulks of large-scale data are avaible and are increasingly grown, from which more information can be mined to gain further information towards human diseases. Our mission is to provide a curated set of methylation information datasets and tools in the human genome, to support and promote research in this area. Especially, we provide a genome-scale landscape to show human methylaton information in a scalable and flexible manner.

The Database for Aligned Ribosomal Complexes (DARC) site provides a resource for directly comparing the structures of available ribosomal complexes.

The site offers a collection of files deposited in the RCSB protein data bank and the Electron Microscopy Data Bank,
which have been aligned so as to make direct comparison of the structures possible.

Publications"The DARC site: a database of aligned ribosomal complexes"

A. Jarasch, P. Dziuk, T. Becker, JP. Armache, A. Hauser, DN. Wilson and Roland Beckmann. Nucleic Acids Res. (2011) (PDF)

COD is a database of crystal structures of small molecules.

canSar is an integrated cancer research and drug discovery resource.

The dbRBC database provides an open, publicly accessible platform for DNA and clinical data related to the human Red Blood Cells (RBC).

The BioSample Database is hosted at EBI and stores information about biological samples used in molecular experiments, such as sequencing, gene expression or proteomics. The goals of the BioSample Database include: (i) recording and linking of sample information consistently within EBI databases such as ENA, ArrayExpress and PRIDE; (ii) minimizing data entry efforts for EBI database submitters by enabling submitting sample descriptions once and referencing them later in data submissions to assay databases and (iii) supporting cross database queries by sample characteristics.

ALFRED is an allele frequency resource for research and teaching. It has been designed to hold data from many sources and make them available over the web. Data are assembled from multiple sources, curated, and entered into the database. Multiple links to other resources are also established by the curators. A variety of search options are available and additional geographic based interfaces are being developed. The database can serve the human anthropologic genetic community by identifying what loci are already typed on many populations thereby helping to focus efforts on a common set of markers. The database can also serve as a model for databases handling similar DNA polymorphism data for other species.