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Resource Guide for Genomics

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UM Research Resources


Genomics Databases and Analysis Tools


General Genomics:
  • Entrez Genome
  • Provides views for a variety of genomes, complete chromosomes, sequence maps with contigs, and integrated genetic and physical maps. Organized in six major organism groups: Archaea, Bacteria, Eukaryotae, Viruses, Viroids, and Plasmids.  Includes complete chromosomes, organelles and plasmids, as well as draft genome assemblies.
  • KEGG: Kyoto Encyclopedia of Genes and Genomes
  • A complete computer representation of the cell, the organism, and the biosphere.  Enables computational prediction of higher-level complexity of cellular processes and organism behaviors from genomic and molecular information.
  • NCBI Genome Biology
  • Provides several genomic biology tools and resources, including organism-specific pages that include links to many web sites and databases relevant to that species.
  • TIGR Comprehensive Microbiology Resource
  • Displays information on all of the publicly available, complete prokaryotic genomes.
Comparative Genomics:
  • Comparative Genometrics
  • Displays for sequenced genomes, three different genometric analyses: the DNA walk and the GC and TA skews during the initial phase.  Primarily focused on prokaryotic chromosomes, but includes genometric information on paradigm plasmids, phages, viruses, and organelles.
  • dbGap – database of Genotypes and Phenotypes
  • Archives and distributes results of studies of the interaction of genotype and phentoype, e.g. genome-wide association studies, medical sequencing, and molecular diagnostic assays, as well as the association betwen genotype and non-clinical traits. 
  • NCBI Map Viewer
  • Provides special browsing capabilities for a subset of organisms in Entrez Genome.
  • SGN – SOL Genomics Network
  • A Clade Oriented Database (COD) containing genomic, genetic, phenotypic and taxonomic information for species in the Euasterid clade, including the families Solanaceae (e.g. tomato, potato, eggplant, pepper, petunia) and Rubiaceae (coffee). Genomic information is presented in a comparative format and tied to the fully-sequenced Arabidopsis genome.
  • UniGene: An Organized View of the Transcriptome
  • Sets of transcript sequences that appear to come from the same transcription locus, together with information on protein similarities, gene expression, cDNA clone reagents and genomic location.
Genomic Sequences:
  • BASyS  - Bacterial Annotation System
  • Performs automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences.
  • Ensembl
  • The Ensembl project produces and makes available genome databases for vertebrates and other eukaryotic species.
  • Provides sequence similarity searching against complete genomes databases using the FASTA (FAST-ALL) programs.
  • KAAS - KEGG Automatic Annotation Server
  • Provides functional annotation of genes by BLAST comparisons against the manually curated KEGG GENES database. The result contains KO (KEGG Orthology) assignments and automatically generated KEGG pathways.
  • UCSC Genome Browser
  • Contains the reference sequence and working draft assemblies for a large collection of genomes, and provides a portal to the ENCODE project.

Non-Human Genomics:
  • BacMap
  • An interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes.
  • CRISPRFinder
  • A gateway to publicly accessible CRISPRs database and software.  Enables easy detection of CRISPRs in locally-produced data and consultation of CRISPRs present in the database.  Includes information on the presence of CRISPR-associated (cas) genes when annotated as such.
  • Drosophila Interactions Database (DroID)
  • A comprehensive gene and protein interactions database designed specifically for the model organism Drosophila.
  • Entrez UniSTS
  • A comprehensive database of sequenced tagged sites (STSs).    
  • GeneDB
  • Provides access to 37 genomes, from various stages of the sequencing curation pipeline, from early access to partial genomes with automatic annotation through to complete genomes with extensive manual curation. 
  • Genome Information Broker for Viruses (GIB-V)
  • A complete virus genome data repository.
  • Genotyping
  • Helps identify the genotype of a viral sequence.
  • HAMAP – High-quality Automated and Manual Annotation of Microbial Proteomes 
  • A system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies.
  • HomoloGene
  • A system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.
  • Influenza Virus Database (IVDB)
  • An integrated information resource and analysis platform for genetic, genomic, and phylogenetic studies of influenza virus.
  • metaTiger
  • A collection of metabolic profiles and phylogenomic information on a taxonomically diverse range of eukaryotes.
  • MGI Mouse Genome Informatics
  • Integrated genetic, genomic and biological data on the laboratory mouse to facilitate the syudy of human health and disease.
  • NCBI Influenza Virus Resources
  • Presents data obtained from the NIAID Influenza Genome Sequencing Project and GenBank, combined with tools for flu sequence analysis, annotation and submission to GenBank.
  • NCBI Viral Genomes
  • A collection of virus genomic sequences. 
  • UCSC Archeal Genome Browser
  • A window on the biology of more than 50 microbial species from the domain Archaea.
  • Yeast Resource Center Public Display Repository
  • Provides access to scientific experimental data resulting from collaborations and technology development involving the Yeast Resource Center.  The data has been made public either through publication or by specific consent of the researchers involved.
  • ZFIN Zebrafish Information
  • The Zebrafish Model Organism Database

DNA Sequence Databases

Coding and Gene Prediction:

  • Gene Index Project
  • An inventory of likely genes and their variants, annotated with information regarding the functional roles played by these genes and their products. Created from available EST (Expressed Sequence Transcripts) and gene sequences, along with the reference genomes wherever available.
  • Genetic Codes at NCBI
  • A comprehensive database that describes genetic codes in various organisms and organelles.
  • The Open Reading Frame Finder (ORF Finder), a graphical analysis tool, finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in the database.
  • A web server for optimizing codon use of DNA sequences.
  • Swiss EMBnet node Server
  • A collection of bioinformatics tools out of Switzerland.

DNA Sequencing and Alignment:

Gene Expression:

  • dPattern: Binding Site Discovery in Human Genome using a Discriminate Pattern Approach
  • Predict TFBS (Transcription Factor Binding Sites) in the promoter regions of up-regulated sequences.
  • GenomeTraFaC
  • A comparative genomics-based resource for initial characterization of gene models and the identification of putative cis-regulatory regions of RefSeq Gene Orthologs.
  • MAPPER2 – Multi-genome Analysis of Positions and Patterns of Elements of Regulation
  • A platform for the computational identification of transcription factor binding sites (TFBSs) in multiple genomes.
  • A software framework for the construction and maintenance of regulatory sequence data annotations. Allows multiple boutique databases to function independently within a larger system (or information mall).
  • A holistic, graphical view of features annotated on nucleotide or protein sequences. This interactive tool highlights the residues in the sequence that correspond to features chosen by the user, and allows easy searching for sequence motifs or extraction of particular subsequences.

Gene Structure:

  • DNAReplication
  • Provides an up to date knowledge base for the eukaryotic DNA replication community.
  • Exon-Intron Database
  • A collection of sequences and annotated information for exons and introns in GenBank.
  • RNA and DNA Folding Applications
  • Contains RNA and DNA folding applications.
  • spliceNest - Visualizing Splicing of Genes from EST Data
  • Mappings of expressed sequences tag (EST) consensus sequences derived from the GeneNest database.
  • A resource for experimentally validated human noncoding fragments with gene enhancer activity from transgenic mice. Most of these noncoding elements were selected for testing based on their extreme conservation with other vertebrates.


Gene Mutations and Diseases


Mutation Analysis:
  • GenePath
  • An application for the analysis of mutant-based experiments and synthesis of genetic networks.
  • Haploview
  • Simplify and expedite the process of haplotype analysis.  Provides a common interface to several tasks relating to such analyses.
  • Protein Mutant Database (PMD)
  • Covers natural as well as artificial mutants, including random and site-directed ones, for all proteins except members of the globin and immunoglobulin families. The PMD is based on literature, not on proteins. That is, each entry in the database corresponds to one article which may describe one, several or a number of protein mutants.
Human Diseases and Mutations:
  • Cancer Genetics Web
  • Comprehensive links to reliable information about genes, their associated proteins, and genetic mutations associated with cancer and related disorders.  Each gene page includes links to major genetic databases and other related sites.
  • Cancer Genome Anatomy Project (CGAP)
  • The goal of NCI's CGAP is to determine the gene expression profiles of normal, precancer, and cancer cells, leading eventually to improved detection, diagnosis, and treatment for the patient.
  • Database of Genomic Variants
  • A curated catalog of structural variation in the human genome in health control samples.  Useful for studies aiming to correlate genomic variation with phenotypic data.
  • Frequency of Inherited Disorders database (FINDbase)
  • A repository of information about the frequency of different mutations leading to inherited disorders in various populations around the globe.
  • GeneSNP Database
  • More than 600 prioritized environmentally relevant gene sequences thought to play a role in susceptibility to environmental exposures.  Integrates gene, sequence and polymorphism data into individually annotated gene models.  A research area of the Environmental Genome Project.
  • The aim of NMD-Chip is to design, develop and validate new sensitive high throughput DNA arrays to efficiently diagnose patients affected by neuromuscular diseases, such as Duchenne / Becker Muscular Dystrophies
Human Proteins:
  • Consensus CDS
  • The Consensus CDS (CCDS) project is a collaborative effort to identify a core set of human and mouse protein coding regions that are consistently annotated and of high quality.
  • Human Mitochondrial Protein Database (HMPDb)
  • Provides data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function.
  • Human Protein Reference Database
  • A centralized platform to visually depict and integrate information pertaining to domain architecture, post-translational modifications, interaction networks and disease association for each protein in the human proteome.
  • Human Unidentified Gene-Encoded (HUGE) Protein Database
  • The HUGE database contains various types of information derived from the predicted primary structure data of newly identified human proteins.
Protein Sequences and Analysis


Alignment Tools:
  • NCBI Protein Database
  • Includes protein entries compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.
  • UniParc (UniProt Archive)
  • Contains only protein sequences but cross-references source databases for other information about the protein.
  • UniProt Knowledgebase(UniProtKB)
  • Consists of Swiss-Prot, a manually annotated and reviewed protein sequence database, and TrEMBL, a computer-annotated supplement of Swiss-Prot that contains all translations of EMBL nucleotide sequence entries not yet integrated in Swiss-Prot and is not reviewed.  A comprehensive, high-quality resource of protein sequence and functional information
Protein Sequence Motifs:

RNA Sequence Databases


RNA Sequencing:
  • BLAT Search Genome
  • BLAT is not BLAST. DNA BLAT works by keeping an index of the entire genome in memory. The index consists of all non-overlapping 11-mers except for those heavily involved in repeats.
  • CorreLogo
  • Generates for a given RNA or DNA sequence alignment a three-dimensional representation in VRML format and JavaView JVX format. 
  • greengenes
  • Align your set of 16S rRNA gene sequences using NAST or find near-neighbors or both.
  • HIV Sequence Database
  • Contains data on HIV genetic sequences, immunological epitopes, drug resistance-associated mutations, and vaccine trials. The website also gives access to a large number of tools that can be used to analyze these data.

  • Reference Sequence (RefSeq)
  • A comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.
RNA Structure and Function:

Gene Therapy


What is Gene Therapy: Genetic Testing Screening Test Information Stem-Cell Research
  • Mayo Clinic
  • Stem Cells: What they are and what they do
  • Medline Plus
  • Overview for consumers about Stem Cells and where they can get even more information regarding the future of stem cell research
  • National Institutes of Health
  • Stem Cell Basics
  • NY Times
  • A free collection of articles about Stem Cells


Calder Library's Genomics Portal offers a varied selection of medical and drug-related information for the benefit of a wide and diverse audience: healthcare professionals, researchers, students and the public at large. This list is not comprehensive. It serves the function of a little black bag of essential resources for bioinformatic and genomic information. For assistance with any of these resources, or to find out about other available research and searching options you can browse the library's full web site, come by the library's Reference Desk or call the Reference, Education & Outreach Services department at (305) 243-6648

We always want your feedback! To suggest additions, corrections or changes to the content of the Calder Library Portal for Drug Information page, please send an email to the Reference, Education & Outreach Services department at reference@med.miami.edu