Ensembl, a genome browser project, produces genome databases for vertebrates, and makes this information freely available online.
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Gene (NCBI) is a searchable database of genes, from RefSeq genomes, and defined by sequence and/or located in the NCBI Map Viewer
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The Genome Data Viewer, NCBI genome browser, allows you to view and search an organism's complete genome, display chromosome maps, and zoom into progressively greater levels of detail, down to the sequence data for a region of interest.
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A major goal of the Encyclopedia of DNA Elements (ENCODE) is to annotate all functional elements of the human genome including protein-coding genes, pseudogenes, and non-coding transcribed loci and to catalog the products of transcription including splice isoforms and regulatory elements that control the cells and circumstances in which a gene is active.
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OMIM (Online Mendelian Inheritance in Man) is a compendium of human genes and genetic phenotypes. The full-text, referenced overviews in OMIM contain information on all known mendelian disorders and over 12,000 genes. OMIM focuses on the relationship between phenotype and genotype.
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The HUGO Gene Nomenclature Committee (HGNC) has assigned unique gene symbols and names to over 33,000 human loci, of which around 19,000 are protein coding. http://genenames.org is a curated online repository of HGNC-approved gene nomenclature and associated resources including links to genomic, proteomic and phenotypic information, as well as dedicated gene family pages.
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Category: Gene information search, Gene expression
WashU Human Epigenome Browser allows: Epigenome
The browser currently hosts Human (and other species) Epigenome Atlas data produced by the Roadmap Epigenomics project,but lets users diverge from the strict genome-centric view of the UCSC browser to, for instance, view all genes (or promoters, or 3’ UTRs) in a given pathway side by side. “You can do lots of Google Maps-style operations, and you can look at your data in the context of their metadata.
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GeneCards maintained by Weizmann Institute of Science is a searchable, integrated, database of human genes that provides concise genomic, transcriptomic, genetic, proteomic, functional and disease related information on all known and predicted human genes.
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The UCSC Genome Browser is an on-line genome browser hosted by the University of California, Santa Cruz (UCSC).[2] [3] It is an interactive website offering access to genome sequence data from a variety of vertebrate and invertebrate species and major model organisms, integrated with a large collection of aligned annotations.
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The Nucleotide database (NCBI) is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.
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The PANTHER (Protein ANalysis THrough Evolutionary Relationships) Classification System is a unique resource that classifies genes by their functions, using published scientific experimental evidence and evolutionary relationships to predict function even in the absence of direct experimental evidence.
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a public archive and repository where nucleotide sequences generated by next-generation sequencing methodologies can be submitted
Category: Gene information search
ENA (European Nucleotide Archive) operates as a public archive and repository where nucleotide sequences generated by next-generation sequencing methodologies can be submitted. Data can be searched interactively and programmatically using free text and sequence similiary search based queries. It is a useful utility also for patent data search.ENA
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EMBL European Bioinformatic Istitute
Category: Gene information search, Protein informations
EBI (EMBL European Bioinformatic Istitute) home page provides a central access point to search several databases for information on genes, proteins, enzymes etc.
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A free extensible and customizable gene annotation portal, a complete resource for learning about gene and protein function (see Wu et al., Genome Biol 10, R130, 2009.)
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HERVd (Human Endogenous Retrovirus DB) is a database compiled from the human genome nucleotide sequences obtained mostly in the Human Genome Projects. It is a relatively simple and fast environment for screening human genome for endogenous retrovirus.
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Gypsy Database (GyDB) is an open editable database devoted to the evolutionary dynamics of viruses and transposable elements based on their phylogenetic classification (Llorens et al., Nucleic Acids Res 39:D70, 2011).
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searchable collection of complete and incomplete large-scale sequencing, assembly, annotation, and mapping projects for cellular organisms
Category: Gene information search
Biomedical search tools
Online genomic tools
Online proteomics tools
Calculators
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Scientific writing/reading
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