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Certain infectious and parasitic diseases

Certain infectious and parasitic diseases.

TransPhylo
Desktop

TransPhylo

A Matlab package based on a Bayesian inference method for reconstructing…

A Matlab package based on a Bayesian inference method for reconstructing transmission events in a densely sampled outbreak using time-labeled genomic data. TransPhylo works by colouring the branches…

TBDB
Dataset

TBDB TuBerculosis DataBase

An online database providing integrated access to genome sequence, expression…

An online database providing integrated access to genome sequence, expression data and literature curation for tuberculosis (TB). TBDB currently houses genome assemblies for numerous strains of…

HIV-1, Human Protein Interaction Database
Dataset
VFDB
Dataset

VFDB Virulence Factor DataBase

Provides up-to-date knowledge of virulence factors (VFs) of various bacterial…

Provides up-to-date knowledge of virulence factors (VFs) of various bacterial pathogens. We recently improved two aspects of the infrastructural dataset of VFDB: (i) removed the redundancy introduced…

HBVdb
Dataset

HBVdb Hepatitis B Virus database

Allows the researchers to investigate the genetic variability of the virus and…

Allows the researchers to investigate the genetic variability of the virus and the viral resistance to treatment.

BacWGSTdb
Dataset

BacWGSTdb

A bacterial whole genome sequence typing database which is designed for…

A bacterial whole genome sequence typing database which is designed for clinicians, clinical microbiologists and hospital epidemiologists. BacWGSTdb borrows the population structure from the current…

g2p-HCV
Web

g2p-HCV geno2pheno-hepatitis-c-virus

An interpretation system to analyse hepatitis C virus (HCV) sequence data with…

An interpretation system to analyse hepatitis C virus (HCV) sequence data with respect to viral subtype and to predict drug resistance. g2p-HCV aligns the input sequences, identifies the genomic…

A A A
HIVed
Dataset

HIVed HIV expression database

Contains curated human proteins with differential expression during the human…

Contains curated human proteins with differential expression during the human immunodeficiency virus (HIV) infection, replication and latency. HIVed aims to display unbiased data reported by authors…

HIVheritability
Desktop

HIVheritability

Estimates the extents to which viral load is heritable either via the viral…

Estimates the extents to which viral load is heritable either via the viral genotype (from donor to recipient) or via the host’s Human Leukocyte Antigen (HLA) genotype. HIVheritability uses linear…

THE REAL McCOIL
Desktop

THE REAL McCOIL

Estimates complexity of infection and population allele frequencies using…

Estimates complexity of infection and population allele frequencies using single nucleotide polymorphism (SNP) data obtained from Sequenom or similar types of SNP assays. THE REAL McCOIL is a Markov…

HepSEQ
Dataset

HepSEQ

A repository for an extensive library of public health and molecular data…

A repository for an extensive library of public health and molecular data relating to hepatitis B virus (HBV) infection collected from international sources.

MapMyFlu
Web

MapMyFlu

Allows to spatially and temporally display influenza viruses related to a query…

Allows to spatially and temporally display influenza viruses related to a query sequence on a Google Map based on BLAST results against the NCBI Influenza Database. Temporal and geographical trends…

A A A
DB-AT
Dataset

DB-AT

Contains transcriptomes of Apicomplexa parasites, as well as datasets…

Contains transcriptomes of Apicomplexa parasites, as well as datasets reflecting a diverse nature of the transcriptomes in individual parasites both in vivo and in vitro. Furthermore, the RNA-Seq…

TrypanoCyc
Dataset

TrypanoCyc

A dynamic database which describes the generic and condition-specific metabolic…

A dynamic database which describes the generic and condition-specific metabolic network of Trypanosoma brucei, a parasitic protozoan responsible for human and animal African trypanosomiasis. In…

SPMM
Web

SPMM Shifted Poisson Mixture Model

A mathematical tool for early HIV-1 evolution within a subject whose infection…

A mathematical tool for early HIV-1 evolution within a subject whose infection originates either from a single or multiple viral variants. SPMM provides a quantitative guideline for segregating viral…

G T A T C G C T A
DeF-GPU
Desktop

DeF-GPU

A graphics processing unit (GPU)-based data mining method. DeF-GPU efficiently…

A graphics processing unit (GPU)-based data mining method. DeF-GPU efficiently and precisely identifies Hepatitis B viral (HBV) deletions from large NGS data, which generally contain millions of…

euHCVdb
Dataset

euHCVdb European Hepatitis C Virus database

A collection of computer-annotated hepatitis C virus (HCV) sequences based on…

A collection of computer-annotated hepatitis C virus (HCV) sequences based on reference genomes. The annotations include genome mapping of sequences, use of recommended nomenclature, subtyping as…

BRD
Dataset

BRD Biosurveillance Resource Directory

A tool to facilitate obtaining disease surveillance information. BRD contains…

A tool to facilitate obtaining disease surveillance information. BRD contains disease surveillance resources, epidemiological models (previously known as the 'BARD'), and a disease…

VecNet-DW
Web

VecNet-DW Vector-Borne Disease Network Data Warehouse

Allows storage, accession, and analysis of malaria-related data scattered in…

Allows storage, accession, and analysis of malaria-related data scattered in heterogeneous forms across many data storage systems. VecNet-DW provides online analytical processing (OLAP)…

TrypsNetDB
Dataset

TrypsNetDB

Provides information to allow a better characterization of the queried proteins…

Provides information to allow a better characterization of the queried proteins in the species of interest. TrypsNetDB is a database that automatically performs inter-species mapping of the available…

sourceR
Desktop

sourceR

Quantifies source attribution in food-borne diseases. sourceR is based on a…

Quantifies source attribution in food-borne diseases. sourceR is based on a Bayesian model that classifies strain types by differential epidemiological behavior and accurately quantifies uncertainty.…

GISAID EpiFlu…
Dataset

GISAID EpiFlu database

Provides a collection of influenza sequences containing associated metadata,…

Provides a collection of influenza sequences containing associated metadata, both clinical and epidemiological. GISAID EpiFlu database is a relational database that stores information about Influenza…

HIV-1…
Dataset

HIV-1 Integrase Inhibitor Database

Contains HIV-1 Integrase (IN) Inhibitors collected from peer-reviewed…

Contains HIV-1 Integrase (IN) Inhibitors collected from peer-reviewed scientific publications. HIV-1 Integrase Inhibitor Database is a manually built database which collects the basic data such as…

tbvar
Dataset

tbvar

Provides a much needed compendium of genomic variants and their annotations for…

Provides a much needed compendium of genomic variants and their annotations for M. tuberculosis complex (MTBC) and provides the first step toward accelerating genotype–phenotype correlations in the…

TDR Targets
Dataset

TDR Targets

Allows to identify and prioritize molecular targets for drug development. TDR…

Allows to identify and prioritize molecular targets for drug development. TDR focuses on pathogens responsible for neglected human diseases. The database includes pathogen specific genomic…

HIVsirDB
Dataset

HIVsirDB

A manually curated database of HIV inhibiting siRNAs that provides…

A manually curated database of HIV inhibiting siRNAs that provides comprehensive information about each siRNA or shRNA. HIVsirDB structure contains sixteen fields including siRNA sequence, HIV…

EPIMIC
Desktop

EPIMIC

A simple and versatile homemade tool, for the real-time systematic automated…

A simple and versatile homemade tool, for the real-time systematic automated surveillance of IDs at Marseille university hospitals, based on the data from our clinical microbiology laboratory,…

Pakistan whole…
Dataset

Pakistan whole genome tuberculosis

Gathers information about tuberculosis. Pakistan whole genome tuberculosis is…

Gathers information about tuberculosis. Pakistan whole genome tuberculosis is an online resource storing different types of stains about tuberculosis disease. This database was based on…

FLUKA
Desktop

FLUKA

Serves for a variety of applications at CERN. FLUKA is a program for…

Serves for a variety of applications at CERN. FLUKA is a program for calculations of particle transport and interactions. It can simulate with high accuracy the interaction and propagation in matter…

BioAfrica
Dataset

BioAfrica

Provides information on Human Immunodeficiency Virus (HIV) proteins. BioAfrica…

Provides information on Human Immunodeficiency Virus (HIV) proteins. BioAfrica is a resource collaborating with Swiss-Prot ViralZone group of the Swiss Institute of Bioinformatics (SIB). The database…

3DFlu
Dataset

3DFlu

Provides information regarding hemagglutinin proteins (HAs) of influenza virus…

Provides information regarding hemagglutinin proteins (HAs) of influenza virus type A. 3DFlu includes non-redundant proteins for which crystal structures are available in the Protein Data Bank (PDB)…

Anti-HIV-Predic…
Web

Anti-HIV-Predictor

Predictes the anti-HIV activity of given compounds. Anti-HIV-Predictor allows…

Predictes the anti-HIV activity of given compounds. Anti-HIV-Predictor allows to discover new anti-HIV agents through drug repositioning of US Food and Drug Administration (FDA) approved drugs. This…

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EbolaVCR
Dataset

EbolaVCR Ebola Virus Computational Resources

In silico resources developed to facilitate scientific community fighting…

In silico resources developed to facilitate scientific community fighting against deadly virus EBOLA. EbolaVCR enlists possible vaccine candidates, therapeutic siRNAs and other related resources.…

FiloBase
Dataset

FiloBase

A comprehensive drug target database for lymphatic filariasis (Lf), one of the…

A comprehensive drug target database for lymphatic filariasis (Lf), one of the oldest and most debilitating tropical diseases. FiloBase models and stores therapeutic targets for Lf. In addition,…

TBXpredict
Desktop

TBXpredict

A computer-aided diagnosis MATLAB toolbox. TBXpredict has been developed for…

A computer-aided diagnosis MATLAB toolbox. TBXpredict has been developed for automated prediction of tuberculosis (TB) from chest X-ray (CXRs) of patients. This software was developed by…

HIVToolbox
Dataset

HIVToolbox

A web system for visual data mining. The original HIVToolbox integrated…

A web system for visual data mining. The original HIVToolbox integrated information for HIV protein sequence, structure, functional sites, and sequence conservation. HIVToolbox2 has new…

EpiDynamics
Desktop

EpiDynamics

Provides a R package which permits to simulate and plot deterministic and…

Provides a R package which permits to simulate and plot deterministic and stochastic models. EpiDynamics allows users to provide mathematical models for infectious diseases in both animals and humans.

EpiModel
Desktop

EpiModel

Offers a R package for procuring a way to construct, solve, and view…

Offers a R package for procuring a way to construct, solve, and view mathematical models related with infectious disease. EpiModel permits users to simulate epidemic models for both pedagogical and…

SInCRe
Dataset

SInCRe Structural Interactome Computational Resource

An integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates…

An integrated database for Mycobacterium tuberculosis H37Rv (Mtb) that collates information on protein sequences, domain assignments, functional annotation and 3D structural information along with…

PDDB
Dataset

PDDB Prion Disease Database

A comprehensive data resource on mouse prion diseases. PDDB contains: (i)…

A comprehensive data resource on mouse prion diseases. PDDB contains: (i) time-course mRNA measurements spanning the interval from prion inoculation through appearance of clinical signs in eight…

SPGDB
Dataset

SPGDB Streptococcus pneumoniae Genome Database

Integrates and analyzes the completely sequenced and available S. pneumoniae…

Integrates and analyzes the completely sequenced and available S. pneumoniae genome sequences. Further, links to several tools are provided to compare the pool of gene and protein sequences, and…

TuberQ
Dataset

TuberQ

A resource aimed for all researchers working on Tuberculosis and specifically…

A resource aimed for all researchers working on Tuberculosis and specifically in the field of target selection and new drug development.

TubercuList
Dataset

TubercuList

Through manual curation, it strives to provide current gene-based information…

Through manual curation, it strives to provide current gene-based information and is thus distinguished from other online sources of genome sequence data for M. tuberculosis.

MyBASE
Dataset

MyBASE

A platform for the functional and evolutionary genomic study of the bacterial…

A platform for the functional and evolutionary genomic study of the bacterial genus Mycobacterium, which is notorious for its two members, Mycobacterium tuberculosis and Mycobacterium leprae, the…

inTB
Dataset

inTB

A web-based system for storage and analysis of clinical, socio-demographic and…

A web-based system for storage and analysis of clinical, socio-demographic and molecular typing data.

LeishCyc
Dataset

LeishCyc

Describes Leishmania major genes, gene products, metabolites, their…

Describes Leishmania major genes, gene products, metabolites, their relationships and biochemical organization into metabolic pathways. LeishCyc provides a systematic approach to organizing the…

KEGG Pathogen
Dataset

KEGG Pathogen

Provides an interface to infectious disease information in KEGG. KEGG Pathogen…

Provides an interface to infectious disease information in KEGG. KEGG Pathogen permits to extract understanding molecular mechanisms of pathogenicity and antimicrobial resistance (AMR) from genomic…

Malaria Data
Dataset

Malaria Data

Provides a fully searchable and downloadable resource for publicly available…

Provides a fully searchable and downloadable resource for publicly available compounds, targets, assays and data for malaria research. Malaria Data is a database that includes compounds from the MMV…

DFVF
Dataset

DFVF Database of Fungal Virulence Factors

Stores known fungal virulence factors. DFVF is an online database that provides…

Stores known fungal virulence factors. DFVF is an online database that provides interactive access to the collected data. The fungus strain taxonomy is recorded with its original reference, as it may…

GuavaH
Dataset

GuavaH Genomic Utility for Association and Viral Analyses in HIV

Provides results from genome-wide association (GWAS) of human immunodeficiency…

Provides results from genome-wide association (GWAS) of human immunodeficiency virus (HIV) disease phenotypes including more than 4,000 individuals. GuavaH includes association results on HIV control…

HCVpro
Dataset

HCVpro Hepatitis C Virus protein interaction database

A comprehensive and integrated HCV-specific knowledgebase housing consolidated…

A comprehensive and integrated HCV-specific knowledgebase housing consolidated information on PPIs, functional genomics and molecular data obtained from a variety of virus databases (VirHostNet,…

NeisseriaBase
Dataset

NeisseriaBase

An online genome and annotation database for Neisseria, a genus consisting a…

An online genome and annotation database for Neisseria, a genus consisting a large group of Gram-negative aerobic commensal of mucosal surface in the human body. Currently NeisseriaBase comprises of…

NNTC
Dataset

NNTC National NeuroAIDS Tissue Consortium

Compiles information about antemortem and postmortem tissues and fluids. NNTC…

Compiles information about antemortem and postmortem tissues and fluids. NNTC collects experimental data as well as Nervous Systems (NS) and peripheral nervous systems (PNS) signs and symptoms or…

MycoCAP
Dataset

MycoCAP Mycobacterium Comparative Analysis Platform

A comparative analysis platform dedicated to the important genus Mycobacterium.…

A comparative analysis platform dedicated to the important genus Mycobacterium. MycoCAP currently provides information of 2108 genome sequences of at least 55 Mycobacterium spp. A number of intuitive…

HPVbase
Dataset

HPVbase

Consists in a web-based resource of the extensively cross-analyzed different…

Consists in a web-based resource of the extensively cross-analyzed different biomarkers involved in human papillomaviruses (HPVs). HPVbase is highly interactive and manually curated. It allows…

FusoBase
Dataset

FusoBase

Fusobacterium are anaerobic gram-negative bacteria that have been associated…

Fusobacterium are anaerobic gram-negative bacteria that have been associated with a wide spectrum of human infections and diseases. FusoBase is an online database providing access to genome-wide…

PB1-F2 Finder
Web

PB1-F2 Finder

Enables scanning of influenza sequences for potential PB1-F2 protein products.…

Enables scanning of influenza sequences for potential PB1-F2 protein products. PB1-F2 Finder provides an initial screen and annotation of PB1-F2 products. The tool is a contribution to the global…

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