Databases and tools

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List of databases and bioinformatics tools developed by researchers in Singapore, description on the content and functions of the databases/tools, and their host institution/organization.

 

Name

Description

Host Institution / Organization

Allergen

Collection allergenic protein records and analytical tools that comply with the Allergen Committee of the International Union of Immunological Societies (IUIS), Food and Agriculture Organisation (FAO) and World Health Organisation (WHO).

I2R

ANTIMIC

ANTIMIC provides a comprehensive repository of known and putative antimicrobial peptides (AMPs) along with the relevant tools so as to facilitate efficient extraction of data and its analysis at molecular level, as well as the search for new AMPs.

I2R

 Burkholderia pseudomallei Genome Database

In silico generation of putative ORFs from B. pseudomallei genome sequence.

NUS-BIC

CasBase

CasBase is an online relational database containing an array of biological data on caspases and their substrates. This database consists of two distinct sets of entries for caspases and their substrates collected web design atlanta from publicly available databases and published literature. Entries are annotated with links to other databases (e.g. Uniprot, PubMed, Interpro, PDB) as well as proprietary data such as substrate cleavage sites and cleavage consequences.

NUS-BIC

Computed ligand binding energy database

A database for facilitating the analysis of Drug Binding Competitveness. It contains information about Computed Ligand-Receptor Interaction Energy and other attributes such as energy components; ligand classification, functions and properties. Ligand structure is also included.

NUS-CSC 

Drosophila melanogaster Exon Database

Database that contains information on Drosophila melanogaster exons presented in a splicing graph form.

NUS-BIC

Drug ADME associated protein database

A database for facilitating the search for drug Absorption, Distribution, Metabolism, Excretion associated proteins. It contains information about known drug ADME associated proteins, functions, similarities, substrates / ligands, tissue distributions, and other properties of the targets.  Associated references are also included.

NUS-CSC

Drug adverse reaction target database

A database for facilitating the search for drug adverse reaction target. It contains information about known drug adverse rection targets, functions and properties. Associated references are also included.

NUS-CSC

ExInt

A database to help to identify common evolutionary patterns in higher eukaryotic genes for the study of intron loss/gain, sliding, splicing, retroposition, recombination, intron/exon duplication, etc.

NTU / NUS-BIC 

Fish pathogen database

Pathogenesis of bacteria (such as Aeromonas hydrophila, Edwardsiella tarda and Vibrio species) and the identification of virulence determinants using fish as a model system for the past six years.

NUS-DBS

HCC-M database

HCC-M database 2D Gel and MALDI Proteomic analysis data.

 NUS-DBS

Hepatitis B registry system 

Web-based Hepatitis B registry system.

NUS-BIC

IE-Kb Intron-Exon Knowledge Base

Intron-Exon Knowledge Base.

NTU / NUS-BIC  

 Kinetic data of biomolecular interactions database

Kinetic Data of Bio-molecular Interaction (KDBI) is a collection of experimentally determined kinetic data of protein-protein, protein-RNA, protein-DNA, protein-ligand, RNA-ligand, DNA-ligandbinding or reaction events described in the literature.

NUS-CSC 

MHCP

The MHC-Peptide Interaction Database (MHCP) is a curated MySQL database for sequence-structure-function information on MHC-Peptide interactions. It contains all structures of Major Histocompability proteins containing bound peptides, with emphasis on the structural characterization of these complexes.

NTU / NUS-BIC

MIDB

MIDB is a database containing all discordant intron positions in homologous genes (MIDB for Mismatched Intron Database) using ExInt, Discordant intron positions are those that are either closely located in homologous genes (within a window of 10 residues) or an intron position that is present in one gene but not in any of its homologs.

NTU / NUS-BIC

Mollusk

Integrated database focusing on the conotoxin sequence information.

I2R

MPID-T

The MHC-Peptide Interaction Database - T-Cell Receptor (MPID-T) is a database for sequence-structure-function information on TCR-peptide-MHC interactions. It contains all structures of TCR-pMHC and pMHC complexes, with emphasis on the structural characterization of these complexes.

NUS-BIC

Scorpion Toxin Database

A molecular database of scorpion toxins.

I2R

SEGE

A database on 'intron less/single exonic' genes from eukaryotes.

NTU / NUS-BIC

Snake Venom Neurotoxin

 A molecular database of snake venom neurotoxins.

I2R / NUS-BCH

Snake Venom PLA2

Specialised database for molecular analysis of snake venom PLA2s, intended to facilitate the design of experimental protocols.

I2R

SPdb

Signal Peptide Database (SPdb) is a database that contains information on signal peptide. The database contains experimentally and non-experimental sequences. This database also contains other information such as amino acid composition, hydropathy plot and more.

NUS-BIC

Splicerator

Integrated Human alternative RNA splicing Database

NUS-DBS

Therapeutic target database

A database to provide information about the known and explored therapeutic protein and nucleic acid targets, the targeted disease, pathway information and the corresponding drugs/ligands directed at each of these targets.

NUS-CSC

XPro

Xpro is a relational database that contains all the eukaryotic protein-encoding DNA sequences in GenBank. It provides detailed and comprehensive features about both the intron containing and the intron-less genes.The current release of Xpro (v.1.2, Jan 2004) is MySQL (v 3.23.39) relational database and contains information up to date with GenBank release 139.

NUS-BIC

SRS

Various tutorials and lectures.

LION bioscience AG

VAGAT

 VAGAT is a Viral Antigenome Analysis Tool for systematic analyses of antigenic diversity from a set of viral protein sequences and mapping their targets of immune response.

I2R

BioSLAX

BioSLAX is a new live CD suite of bioinformatics tools has been released by the resource team of the BioInformatics Center (BIC), National University of Singapore (NUS). Bootable from any PC, this CD runs the compressed SLACKWARE flavour of the LINUX operating system also known as SLAX.

NUS-BIC

APBioKnoppix

The original APBioBox project was an APBioNet project supported through a grant from the International Development Research Centre (IDRC) of Canada from 2002-2003 and hosted in the Dept. of Biochemistry, National University of Singapore (NUS).

NUS-BIC

APBioKnoppix2

APBioKnoppix2 is a remaster of the popular Knoppix (specifically version 4.02) and it has since been deployed in the use of teaching and training.

NUS-BIC

MULTIPRED

MULTIPRED is a computational system for prediction of peptides binding to multiple molecules belonging to human leukocyte antigen (HLA) class I A2, A3 and class II DR supertypes.

I2R

CysView

CysView is a tool facilitating the grouping of entries in a database (Swissprot or GenBank format-based) by similar disulfide bridge patterns, 'disulfide connectivity patterns'. I2R
FIMM FIMM,  is an integrated database of functional immunology, focusing on MHC, antigens, T- and B-cell epitopes, and diseases. I2R
BoLAdB BoLA dB is an integrated database, focusing on MHC genetics of the cow. I2R
BioWare BioWare is a suite of 4 data warehousing modules for the retrieval, annotation and publishing of specialist molecular databases. I2R
Gene Expression Datasets   The site provides tools to convert biological datasets (in particular gene expression data) into different formats I2R
InterWeaver
InterWeaver is a web server of Interaction Reports. It aims to help biologists discover potential protein interaction partners from various online resources and prediction methods. I2R
 ADVICE
ADVICE is a web server providing Automated Detection and Validation of Interaction based on the Co-Evolutions between interacting proteins. I2R
InterDom
InterDom is a database of putative interacting protein domains derived from multiple sources, ranging from domain fusions (Rosetta Stone), protein interactions (DIP and BIND), protein complexes (PDB), to scientific literature (MEDLINE). I2R
NSDPath  Nervous System Disease Pathweaver (NSDPath) is a database of disease-specific gene association networks specialized in nervous diseases. I2R
Dragon Genome Explorer Promoter prediction system and transcription region analysis. I2R
Dragon Promoter Finder 1.5  This tools helps identify promoter in genomes. I2R
Dragon Gene Start Finder 1.0  This tools helps identify start sites of genes. I2R
Dragon GC+ Promoter Finder 1.0  This tools helps identify promoters in genomes. I2R
Dragon Motif Builder 1.0  System for Discovery and Building Motifs in DNA Sequences. I2R
Dragon ERE Finder 2.0 System for Identification and Interactive Analyses of Estrogen Response Elements in DNA Sequences. I2R
FIE2.1
5'-end Information Extraction. I2R
ICE database
Information for the coordinates of exons. I2R
Dragon TF Association Miner v.2 A system for mining potential associations between transcription factors, gene ontology categories, and diseases, from  free-text documents. I2R
Dragon Metabolome Explorer System for exploring potential associations in the metabolic networks (pathways, enzymes and metabolites),  ontologies (anatomy, developmental stages) and genes in Arabidopsis thaliana and other plants, based on mining PubMed documents. I2R
Dragon Disease Explorer System for exploring potential associations of diseases, transcription factors and gene ontology categories (anatomy, cell type, developmental stages, pathology) as contained in eVoc ontologies, based on mining PubMed documents. I2R
Dragon Estrogen Responsive Genes Database
Estrogen responsive genes database. I2R
Dragon REGULOME (Hs) Database A database of transcriptional regulatory patterns found in human promoters contained in the Eukaryotic Promoter Database (EPD). I2R
Dragon TF Integrator A web resource that allows biologists to inspect and evaluate different information related to transcription factor (TF) functionality. I2R
Estrogen Response Element Finder A system for Locating Estrogen Response Elements in DNA Sequences. I2R
BioDArt A catalogue of biological data artifacts. I2R
AllerTool AllerTool is a web server providing integrated tools useful for assessment of allergenicity and allergic cross-reactivity of protein sequences. I2R
CandiVF Candida albicans Virulence Factor Database. I2R
PREDNOD A prediction server for peptide binding to the H-2g7 haplotype of the non-obese diabetic mouse. I2R
PRED(TAP) A system for prediction of peptide binding to the human transporter associated with antigen processing. I2R
PREDBALB/c A system for the prediction of peptide binding to H2d molecules, a haplotype of the BALB/c mouse. I2R
ESPript ESPript, Easy Sequencing in Postscript, is a utility to generate a pretty PostScript output from aligned sequences. NUS-BIC 
GO Module Analyser Go-Module Analyser is a Java 3D based program that visualizes the Go Modules on the protein structures and dynamically analyses the relation between the go-module boundaries and intron position in eukaryotic homologues. NUS-BIC
JEMBOSS Portal Java Emboss Portal. NUS-BIC
MGAlign MGAlign (short for mRNA to Genome Alignments) is a webservice to quickly and accurately align mRNA sequences to genomic sequences on a personal computer. NUS-BIC
BLAST Web Portal BLAST Web Portal. NUS-BIC
 ClustalW Web Portal
ClustalW Web Portal for Running Multiple Sequence Alignment. NUS-BIC
MoViES Molecular vibrations evaluation server. NUS-CSC 
SCOP (Local Mirror) Structural Classification of Proteins Mirror. NUS-BIC 
SDPMOD A web service for comparative modelling of small disulphide-bonded proteins. NUS-BIC 
Sequence Manipulation Suite (SMS) The Sequence Manipulation Suite is a collection of JavaScript programs for generating, formatting, and analyzing short DNA and protein sequences. NUS-BIC
SGM Splicing Graph Modules (SGM) is a collection of Python modules housed within a Python package to draw splicing graphs (a form of visual representation of several transcript sequences which may exhibit alternative splicing). NUS-BIC
SRS  Sequence Retrieval System from primary databases. NUS-BIC
SVMProt Protein function prediction software. NUS-CSC
XdomView (Version 2.1) A Graphical Tool for Protein Domain and Exon Position Visualization. NUS-BIC
WEMBOSS Emboss Web Portal. NUS-BIC
WEMBOSS II Emboss Web Portal - with personal login and disk space. NUS-BIC
P53 Knowledgebase An integrated resource to facilitate p53 research. BII


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