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Welcome to the Calder Portal for Genomics
Navigate to:
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Genomics Databases and Analysis Tools |
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General Genomics:
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.
Comprehensive data repository of complete microbial 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.
Provides several genomic biology tools and resources, including organism-specific pages that include links to many web sites and databases relevant to that species.
Displays information on all of the publicly available, complete prokaryotic genomes.
Comparative Genomics:
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.
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.
Provides special browsing capabilities for a subset of organisms in Entrez Genome.
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.
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:
Performs automated, in-depth annotation of bacterial genomic (chromosomal and plasmid) sequences.
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.
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.
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:
An interactive visual database containing hundreds of fully labeled, zoomable, and searchable maps of bacterial genomes.
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.
A comprehensive gene and protein interactions database designed specifically for the model organism Drosophila.
A comprehensive database of sequenced tagged sites (STSs).
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.
A complete virus genome data repository.
Helps identify the genotype of a viral sequence.
A system, based on manual protein annotation, that identifies and semi-automatically annotates proteins that are part of well-conserved families or subfamilies.
A system for automated detection of homologs among the annotated genes of several completely sequenced eukaryotic genomes.
An integrated information resource and analysis platform for genetic, genomic, and phylogenetic studies of influenza virus.
A collection of metabolic profiles and phylogenomic information on a taxonomically diverse range of eukaryotes.
Integrated genetic, genomic and biological data on the laboratory mouse to facilitate the syudy of human health and disease.
Presents data obtained from the NIAID Influenza Genome Sequencing Project and GenBank, combined with tools for flu sequence analysis, annotation and submission to GenBank.
A collection of virus genomic sequences.
A window on the biology of more than 50 microbial species from the domain Archaea.
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.
The Zebrafish Model Organism Database
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DNA Sequence Databases |
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Coding and Gene Prediction:
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.
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.
A collection of bioinformatics tools out of Switzerland.
DNA Sequencing and Alignment:
Compare your query sequence to the working draft sequence of the human genome or its mRNA and protein products.
Map your sequence to the genome.
Generates for a given RNA or DNA sequence alignment a three-dimensional representation in VRML format and JavaView JVX format.
A collection of sequences from many sources, including GenBank, RefSeq, and PDB.
Translate from DNA/RNA sequences to a protein sequence.
Binary, multiple and alignment analysis tools.
Compare nucleotide or protein sequences to sequence databases and calculate the statistical significance of matches.
Gene Expression:
Predict TFBS (Transcription Factor Binding Sites) in the promoter regions of up-regulated sequences.
A comparative genomics-based resource for initial characterization of gene models and the identification of putative cis-regulatory regions of RefSeq Gene Orthologs.
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:
Provides an up to date knowledge base for the eukaryotic DNA replication community.
A collection of sequences and annotated information for exons and introns in GenBank.
Contains RNA and DNA folding applications.
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.
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Gene Mutations and Diseases |
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Mutation Analysis:
An application for the analysis of mutant-based experiments and synthesis of genetic networks.
Simplify and expedite the process of haplotype analysis. Provides a common interface to several tasks relating to such analyses.
Detect substitution and indel SNPs in sequencing traces.
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:
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.
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.
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.
A repository of information about the frequency of different mutations leading to inherited disorders in various populations around the globe.
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:
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.
Provides data on mitochondrial and human nuclear encoded proteins involved in mitochondrial biogenesis and function.
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.
The HUGE database contains various types of information derived from the predicted primary structure data of newly identified human proteins.
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Protein Sequences and Analysis |
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Alignment Tools:
Includes protein entries compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.
Contains only protein sequences but cross-references source databases for other information about the protein.
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
Facilitates sequence merging in UniProt and allows faster and more informative sequence similarity.
Protein Sequence Motifs:
Predicts potential protein post-translational modifications (PTMs) and finds potential single amino acid substitutions in peptides.
A list of the proteomics tools.
Predicts RNA binding residues in proteins.
Searches the protein sequences against the MOTIF library.
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RNA Sequence Databases |
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RNA Sequencing:
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.
Generates for a given RNA or DNA sequence alignment a three-dimensional representation in VRML format and JavaView JVX format.
Align your set of 16S rRNA gene sequences using NAST or find near-neighbors or both.
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.
A database of Metal Ion Binding Sites in RNA.
A comprehensive, integrated, non-redundant, well-annotated set of sequences, including genomic DNA, transcripts, and proteins.
RNA Structure and Function:
Information about the structure of the ribosome.
Makes visualization of RNA pseudoknots easier.
Contains RNA and DNA folding applications.
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Gene Therapy |
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What is Gene Therapy:
A guide for consumers to understand genetics
Question and Answers from the National Cancer Institute on the future of gene therapy as a treatment for cancer
Information from the Human Genome Project about Gene Therapy
Genetic Testing
Basic information on genetic testing
A worksheet about the basics in genetic testing
Frequently Asked Questions About Genetic Testing
Screening Test Information
Information about At-Home Genetic Testing
Information about Pre-Natal Genetic Screening
Gene Testing
BRCA1 and BRCA2: Cancer Risk and Genetic Testing
Genetic Testing: How it is used for Healthcare
Parentage Testing
Stem-Cell Research
Stem Cells: What they are and what they do
Overview for consumers about Stem Cells and where they can get even more information regarding the future of stem cell research
Stem Cell Basics
A free collection of articles about Stem Cells
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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
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