LibGuides: Bioinformatics: Home

Welcome

Click on the tabs below to access each sub-discipline. For each resource, if you click on the title you will be directed to a page with an extended description, links to tutorials, and additional information regarding operating and supporting institutions of each resource.

Databases

Cambridge Structural Database (CSD)
The CSD offers a collection of molecular structures generated through X-Ray Crystallography
Golm Metabolome Database (GMD)
The GMD is a database of Gas Chromatography/Mass Spectroscopy data on biologically relevant metabolic products
Human Autophagy Database
Database of genes and proteins associated with the process of autophagy in humans
Human Metabolome Database (HMD)
The HMD is a database of human metabolites and their associated chemical and biological data
Kyoto Encyclopedia of Genes and Genomics
KEGG is a vast database containing human genetic information as well as how those genes encode for proteins, their involvement in biochemical pathways, their role in disease and many other medically and biologically relevant information
neXtProt
An annotated database of about 20,000 human proteins with structural, functional, localization and pathway information
Non-B DB
Database of instances in which DNA has been found in the non-standard B-DNA form
Protein Data Bank (PDB)
Database of 3D models of proteins, nuclotides, and complexes
Protopedia
Wiki style database of protein containing general information and structural data
Reactome
Database of known human reaction pathways
STRING
Database of protein-protein interactions from a multitude of species
SuperPose
Online tool to identify superpositioning and similarity in proteins
SuperSweet
Database of artificial and natural sweeteners with relevant biological and chemical information
T3DB (Toxin and Toxin Target Database)
Database of a wide array of toxic molecules, with information relating to their targets, mechanisms of action, toxicity profiles, and relevant medical information
ThYme
Database of enzymes involved in fatty acid and polyketide synthesis as well as enzymes acting on thioester containing substrates
TopFIND
Database of information on the structure of the C- and N-termini of proteins along with information on protease processing
WikiPathways
Wiki style database of biological pathways in a multitude of species with the ability to search based on condition, gene/protein, and type of pathway

Human Autophagy Database
Database of genes and proteins associated with the process of autophagy in humans
Human Protein Atlas
The Human Protein Atlas serves as a reference to proteins and the other proteins they associate with. In addition to protein-protein interactions it serves to show cellular and tissue localization, pathological associations, cell lineage and localization, tissue localization, and pathology at the cellular and tissue level
neXtProt
An annotated database of about 20,000 human proteins with structural, functional, localization and pathway information
Protein Data Bank (PDB)
Database of 3D models of proteins, nuclotides, and complexes
Protopedia
Wiki style database of protein containing general information and structural data
STRING
Database of protein-protein interactions from a multitude of species
SuperPose
Online tool to identify superpositioning and similarity in proteins
ThYme
Database of enzymes involved in fatty acid and polyketide synthesis as well as enzymes acting on thioester containing substrates
WikiPathways
Wiki style database of biological pathways in a multitude of species with the ability to search based on condition, gene/protein, and type of pathway

AmoebaDB
Database of the genomes of Entamoeba and Acanthamoeba parasites
Animal Genome Size Database
Database containing information on the genomic size of animal species
BacMap
Database of the genomes of bacterial and archaeal species
GeneCards
GeneCards is a database of known and predicted human genes. It contains genomic, proteomic, transcriptomic, functional and clinical information
GeneDB
GeneDB collects genetic information for a multitude of Protozoan, Helminth, and Fungi species
GWASdb
GWASdb is a database of single-nucleotide polymorphisms (SNP's) associated with disease states identified in Genome Wide Association Studies
Human Autophagy Database
Database of genes and proteins associated with the process of autophagy in humans
Kyoto Encyclopedia of Genes and Genomics
KEGG is a vast database containing human genetic information as well as how those genes encode for proteins, their involvement in biochemical pathways, their role in disease and many other medically and biologically relevant information
The Monarch Initiative
Database connecting diseases, genetic variation, phenotypes, and model organisms in an attempt to improve the treatment of human disease
Mutation Taster
An online resource to predict the outcome of mutations in genes or short segments of DNA
Non-B DB
Database of instances in which DNA has been found in the non-standard B-DNA form
PharmGKB
Pharmacogenomics database allowing for integration of drug mechanisms and the impact of genetic variation on the effect of those drugs
PomBase
Genetic and proteomic database of the fission-yeast model organism S. pombe
Saccharomyces Genome Database
Genomic database of the yeast model organism S. cerevisiae
TargetScan
Database of predicted and known microRNA targets in mammals
TDR Targets
Database of interactions between drug's and their targets
tRNADB
Database of tRNA genes in predominantly prokaryotic species, with a small collection of eukaryotic and organelle coded tRNA's
UCSC Genome Database
Database of complete genomes of a multitude of animal species ranging from H. sapiens, M. musculus, Canis, D. rerio, and C. elegans. One viral genome included (Filoviridae ebolavirus Sierra Leone)

AmoebaDB
Database of the genomes of Entamoeba and Acanthamoeba parasites
BacMap
Database of the genomes of bacterial and archaeal species
GeneDB
GeneDB collects genetic information for a multitude of Protozoan, Helminth, and Fungi species
MycoBank
A database of fungal phylogeny and a source to deposit new species
PhagesDB
Database of bacteriophages
PHI-base
Database of interaction between pathogens and their hosts
PhytoPath
Database of relevant plant pathogens and the phenotypes associated with those pathogens
PlasmoDB
Database of the genetics of Plasmodium spp
Pseudomonas Genome Database
Genomic database of Pseudomonas spp. allowing for strain specific searches
ViralZone
Database of viral species with information on viral evolutionary relationship, host-viral interactions, viral molecular biology, viral entry and exit, and more
Virus Pathogen Database and Analysis Resource
Database of viruses with information on strain differences, phylogenetic relations, protein structure and function, and antiviral drugs

The Arabidopsis Information Resource (TAIR)
Database of genomic and molecular information of the plant model organism A. thaliana
Candida Genome Database
The Candida Genome Database is a collection of experimentally determined genome sequences and protein information in C. albicans and other species
DictyBase
DictyBase is a database of the genome of the slime mold model organism D. discoideum as well as other related species
FlyBase
FlyBase is a genomic database relating to the model eukaryotic organism Drosophila. In addition to genes, it provides RNA and Protein data
Mouse Genome Database
Database of genetic and proteomic data for M. musculus
Mouse Phenome Database
A database of the phenotypic changes associated with genetic variation and experimentation in M. musculus
PlasmoDB
Database of the genetics of Plasmodium spp
PomBase
Genetic and proteomic database of the fission-yeast model organism S. pombe
Rat Genome DB
Database of genes, diseases, proteomic, and phenotypic variation of Rattus spp. Additionally has information for Chinchilla spp.
Saccharomyces Genome Database
Genomic database of the yeast model organism S. cerevisiae
WormBase
Nematode genetics database
Xenobase
Database of genes, gene expression, experimental protocols, and species stocks of the vertebrate model organisms Xenopus spp.
Zebrafish Information Network
Database of genetics, proteomics, and mutant strains of the model organism Z. rino

FooDB
FooDB is a database contanintg the composition, chemical, and biological information of a wide array of foods
SuperSweet
Database of artificial and natural sweeteners with relevant biological and chemical information

DrugBank
DrugBank is a pharmacological database that combines information on pharmaceutical and other drugs with their experimentally determined mechanism of action
Guide to Pharmacology
A database of currently identified pharmaceutical targets and the drugs that target them
The Monarch Initiative
Database connecting diseases, genetic variation, phenotypes, and model organisms in an attempt to improve the treatment of human disease
TDR Targets
Database of interactions between drug's and their targets

The Arabidopsis Information Resource (TAIR)
Database of genomic and molecular information of the plant model organism A. thaliana
PhytoPath
Database of relevant plant pathogens and the phenotypes associated with those pathogens

T3DB (Toxin and Toxin Target Database)
Database of a wide array of toxic molecules, with information relating to their targets, mechanisms of action, toxicity profiles, and relevant medical information

Animal Diversity Web
A database on the classification, distribution, and biology of animal species
Animal Genome Size Database
Database containing information on the genomic size of animal species
IUCN Red List
The Red List is a database of species that are at the risk of extinction in the wild or are trending on a dangerous path towards population instability. It provides biological and conservation information on the species in the list
Mouse Genome Database
Database of genetic and proteomic data for M. musculus
Mouse Phenome Database
A database of the phenotypic changes associated with genetic variation and experimentation in M. musculus
Rat Genome DB
Database of genes, diseases, proteomic, and phenotypic variation of Rattus spp. Additionally has information for Chinchilla spp.
TreeFam
Database of phylogenetic trees of organisms using both known and predicted genomic information
Xenobase
Database of genes, gene expression, experimental protocols, and species stocks of the vertebrate model organisms Xenopus spp.
Zebrafish Information Network
Database of genetics, proteomics, and mutant strains of the model organism Z. rino

Funding

RRLC Internship Program

The creation of this Bioinformatics guide was generously funded by the Rochester Regional Library Council (RRLC). Jareth Wischmeyer was selected as a participant in the 2018-2019 RRLC Paid Internship Program. He graduated from Fisher in the Spring of 2019 with a B.S. in Pharmaceutical Chemistry.