Bioresearch Portal - Lane Medical Library & Knowledge Management Center

Bioresearch » Tools & Databases

Genomes & Homology
- Ensembl Genome Browser | A genome browser provided by the European Molecular Biology Institute
- NCBI Genome Browser | A genome browser provided by the NCBI
- UCSC Genome Browser | A genome browser curated by UCSC | Videos
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MGD: Mouse Genome Database | Mouse genome informatics database from The Jackson Labs

RGD: Rat Genome Database | Rat genome informatics database by PhysGen Knockouts

TAIR: The Arabidopsis Information Resource | Arabidopsis thaliana genome database

CGD: Candida Genome Database | Candida albicans genome database | SD

CMR: Comprehensive Microbial Repository | Comprehensive prokaryotic genome database

Flybase | A database for Drosophila genes and genomes

HomoloGene | A system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes

HOVERGEN | Homologous Vertebrate Gene Database

SGD: Saccharomyces genome database | Saccharomyces cerevisiae (baker's yeast) genome database | SD

The S. pombe Genome Project | Schizosaccharomyces pombe (fission yeast) genome sequencing project

TGD: Tetrahymena Genome Database | Tetrahymena thermophila genome database at the Institute of Genomic Research | SD

WormBase | C. elegans and related nematodes genomes database

ZFIN | Danio rerio (Zebra fish) genome database

PCR, Cloning and Sequence Analysis
- Oligo | Primer analysis software for polymerase chain reaction (PCR), sequencing, site-directed mutagenesis, and various hybridization applications | CMGM
- Gene Construction Kit | Cloning/vector construction downloadable software | CMGM
- MacVector | All purpose DNA/Protein sequence analysis software | CMGM
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Biology Workbench | Web based molecular biology tool | SL

BioWareDB | Specialized search engine for identifying life sciences software programs or databases to support bioresearch

DNASTAR Lasergene 8.1.3 | Comprehensive DNA and protein sequence analysis software suite | CMGM

DNAStrider | Easy to use DNA sequence mapping, editing and analysis tool | CMGM

EMBOSS | Open source software package for classical molecular biological analytical tasks

Gene Construction Kit | Cloning/vector construction downloadable software

Geneious Pro | General Sequence analysis tool | CMGM

MacClade 4.08 | Phylogenetic analysis tool using parsimony | CMGM

NextBio | A biological information search engine [Enterprise-level trial access]

Sequencher | Sequence fragment assembly software

SOURCE | A data unification tool spanning multiple scientific databases | SD

Sybyl 8.1 | Molecular modeling suite | CMGM

Vector NTI | High-powered yet reasonably easy to use tool for creating cloning vectors | CMGM

Gene Expression & Function
- GeneCards | Searchable, integrated, database of human genes that provides concise genomic related information
- 5'SAGE | Specialized database that compiles mRNA transcript start site data
- BRENDA | Comprehensive enzyme information system
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BioCyc | A collection of 1004 Pathway/Genome Databases | Videos

BioGPS | A freely available gene annotation portal

BioProspector | A tool for discovering conserved DNA motifs in upstream regulatory regions of co-expressed genes | SD

BodyMap | A data bank of expression information of human and mouse genes

CompareProspector | DNA motif prediction tool | SD

dbSNP | NCBI database of Single Nucleotide Polymorphisms

Eureka by GeneGo | Knowledge mining program that allows patrons to quickly find high quality, relevant answers from a manually curated biological database | summary

GPCRDB | Molecular-Specific Information System for G Protein-Coupled Receptors

Bioinformatik Harvester | Metasearch engine spanning a large collection of bio-oriented data sources which assembles the individual search results into one long page for easy scanning

iHOP | A Gene Function mapping tool from the literature

ImMunoGeneTics | A collection of integrated databases specializing in Immunoglobulins, T cell receptors and the Major Histocompatibility Complex (MHC) of all vertebrate species

KEGG | Integrated database resource consisting of 16 main databases, broadly categorized into systems, genomic, and chemical informations

MEGA: Molecular Evolutionary Genetic Analysis | A windows based tool for conducting automatic and manual sequence alignment, inferring phylogenetic trees, mining web-based databases, estimating rates of molecular evolution, inferring ancestral sequences, and testing evolutionary hypotheses

The MEME Suite | Motif based sequence analysis tools

NucleaRDB | A Molecular-Specific Information System for Nuclear Receptors

PubGene | Graphical Go/PubMed gene associations

UTRdb | Untranslated transcript sequences

Prion Disease DB | Molecular-Specific Information System for Prion proteins

KChannelDB | Molecular-Specific Information System for potassium channels

GPCRIPDB Molecular-Specific Information System for GPCR Interacting Partners (G proteins & RAMPs)

Chemistry & Proteomics
- BIOBASE Knowledge Library | curated protein data (formerly PROTEOME) | summary | Videos | SL
- UniProt | Principal repository of protein sequences & function data
- PharmGKB | Integrated resource about how variation in human genetics leads to variation in response to drugs Videos
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Accelrys DiscoveryViewer | A free windows based biomolecular structure viewer application (more capable pro version available)

BIND: Biomolecular Interaction Network Database | Curated descriptions of protein interactions, molecular complexes and pathways

CATH: Class Architecture Topology and Homologous | A database providing hierarchial structure of protein domains

Cn3D | A molecular structure viewer by NCBI | Videos

DIP: Database of Interacting Proteins | A database of experimentally determined protein interactions

DiscoveryGate | MDL chemistry & pharmacology search engine | SL | Videos

DrugBank | Comprehensive drug and drug target data

ExPASy | Proteomics databases and tools of the Swiss Institute of Bioinformatics

FistGlance | A simple tool for macromolecular visualization

NCBI MMDB | NCBI Molecular Modeling Database | summary

RCSB PDB | An archive of experimentally-determined structures of proteins, nucleic acids, and complex assemblies

PRIDE: Protein and Peptide Identification | A proteomics data repository

RasMol | A browser plug-in for viewing biomolecular structures

SCOP: Structural Classification of Proteins

UnitProt

LOCATE | Predicted protein localization & structure tool

MiRNa Resources
- miRbase | Searchable database of published miRNA sequences and annotation
- miRNAMap | Database of experimentally verified microRNAs and miRNA target genes in human, mouse, rat, and other metazoan genomes
- microRNA.org | Comprehensive resource of microRNA target predictions and expression profiles
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miR2Disease | Comprehensive manually curated database of miRNA deregulation in human diseases

miRecords | Resource for animal miRNA-target interactions

miRGator | Database for functional interpretation of miRNAs

miRGen | integrated database of positional relationships between animal miRNAs (and their targets) and genomic annotation sets

miROrtho | Database of predictions of precursor miRNA genes covering several animal genomes combining orthology and a Support Vector Machine

Targetscan | Online software provided by MIT for prediction of microRNA targets

High Throughput Data Analysis
- PANTHER | Protein classification & expression analysis database
- GeneSpring | Microarray data analysis software | CMGM | Videos
- SAM: Significance analysis of microarrays | An Excel add-in for analyzing microarray data | SL | SD
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eBioinformatics | A bioinformatics software package formatted for easy installation on Mac OS X

Partek | Genomic data analysis software suite | CMGM

GEO: Gene Expression Omnibus | NCBI's microarray data repository | summary | Videos

GO: Gene Ontologies | A database aiming to standardize the representation of gene and gene product attributes across species and databases | Videos | SD

GoMiner | Omics data interpretation tool

Ingenuity Pathways Analysis | A curated database and analysis system for understanding how proteins work together to effect cellular changes| CMGM | Videos

MS Visio | Diagramming tool

MeV: Microarray multiexperiment Viewer | A desktop application for the analysis, visualization and data-mining of large-scale genomic data

SMD: Stanford Microarray Database | Stanford University's microarray data repository | Videos | SD

StepMiner | A temporal microarray gene analysis tool | SD

MetaCore by GeneGo | A curate and integrated knowledge database and software suite for pathway analysis of experimental data and gene lists

Array Express | The European Bioinformatics Institute's microarray data repository

Cisgenome | An integrated tool for tiling array, ChIP-seq, genome and cis-regulatory element analysis | SD

Image Analysis
- ImageJ | General purpose image analysis for gels and blots from NIH
- ImageQuant | General purpose image analysis for gels and blots from Molecular Dynamics
- Springer Images | A growing collection of scientific images that spans the scientific, technical and medical fields, including imagesMD | SL
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Imaris 7 | CMGM

Kodak 1D Image Analysis | General purpose image analysis for gels and blots from Kodak | CMGM

Noesys 2.0 | A most complete scientific-visualization program for large scientific, medical, or engineering images | CMGM

OsiriX | 3-D medical imaging software for CT, MRI and confocal microscopy | CMGM

ScreenCalipers | Measure distances on your screen (pixels, mm, etc.) | CMGM

Metamorph | General purpose image analysis from Molecular Devices