Genomes & Maps
A database providing information on the structure of assembled genomes, assembly names and other meta-data, statistical reports, and links to genomic sequence data.
- BioProject (formerly Genome Project)
A collection of genomics, functional genomics, and genetics studies and links to their resulting datasets. This resource describes project scope, material, and objectives and provides a mechanism to retrieve datasets that are often difficult to find due to inconsistent annotation, multiple independent submissions, and the varied nature of diverse data types which are often stored in different databases.
- Database of Genomic Structural Variation (dbVar)
The dbVar database has been developed to archive information associated with large scale genomic variation, including large insertions, deletions, translocations and inversions. In addition to archiving variation discovery, dbVar also stores associations of defined variants with phenotype information.
Contains sequence and map data from the whole genomes of over 1000 organisms. The genomes represent both completely sequenced organisms and those for which sequencing is in progress. All three main domains of life (bacteria, archaea, and eukaryota) are represented, as well as many viruses, phages, viroids, plasmids, and organelles.
- Genome Reference Consortium (GRC)
The Genome Reference Consortium (GRC) maintains responsibility for the human and mouse reference genomes. Members consist of The Genome Center at Washington University, the Wellcome Trust Sanger Institute, the European Bioinformatics Institute (EBI) and the National Center for Biotechnology Information (KOK体育官方网站). The GRC works to correct misrepresented loci and to close remaining assembly gaps. In addition, the GRC seeks to provide alternate assemblies for complex or structurally variant genomic loci. At the GRC website (http://www.genomereference.org), the public can view genomic regions currently under review, report genome-related problems and contact the GRC.
- HIV-1, Human Protein Interaction Database
A database of known interactions of HIV-1 proteins with proteins from human hosts. It provides annotated bibliographies of published reports of protein interactions, with links to the corresponding PubMed records and sequence data.
- Influenza Virus
A compilation of data from the NIAID Influenza Genome Sequencing Project and GenBank.聽 It provides tools for flu sequence analysis, annotation and submission to GenBank. This resource also has links to other flu sequence resources, and publications and general information about flu viruses.
- KOK体育官方网站 Pathogen Detection Project
A project involving the collection and analysis of bacterial pathogen genomic sequences originating from food, environmental and patient isolates. Currently, an automated pipeline clusters and identifies sequences supplied primarily by public health laboratories to assist in the investigation of foodborne disease outbreaks and discover potential sources of food contamination.
- Nucleotide Database
A collection of nucleotide sequences from several sources, including GenBank, RefSeq, the Third Party Annotation (TPA) database, and PDB. Searching the Nucleotide Database will yield available results from each of its component databases.
Database of related DNA sequences that originate from comparative studies: phylogenetic, population, environmental and, to a lesser degree, mutational. Each record in the database is a set of DNA sequences. For example, a population set provides information on genetic variation within an organism, while a phylogenetic set may contain sequences, and their alignment, of a single gene obtained from several related organisms.
A public registry of nucleic acid reagents designed for use in a wide variety of biomedical research applications, together with information on reagent distributors, probe effectiveness, and computed sequence similarities.
- Retrovirus Resources
A collection of resources specifically designed to support the research of retroviruses, including a genotyping tool that uses the BLAST algorithm to identify the genotype of a query sequence; an alignment tool for global alignment of multiple sequences; an HIV-1 automatic sequence annotation tool; and annotated maps of numerous retroviruses viewable in GenBank, FASTA, and graphic formats, with links to associated sequence records.
- SARS CoV
A summary of data for the SARS coronavirus (CoV), including links to the most recent sequence data and publications, links to other SARS related resources, and a pre-computed alignment of genome sequences from various isolates.
- Sequence Read Archive (SRA)
The Sequence Read Archive (SRA) stores sequencing data from the next generation of sequencing platforms including Roche 454 GS System庐, Illumina Genome Analyzer庐, Life Technologies AB SOLiD System庐, Helicos Biosciences Heliscope庐, Complete Genomics庐, and Pacific Biosciences SMRT庐.
- Trace Archive
A repository of DNA sequence chromatograms (traces), base calls, and quality estimates for single-pass reads from various large-scale sequencing projects.
- Viral Genomes
A wide range of resources, including a brief summary of the biology of viruses, links to viral genome sequences in Entrez Genome, and information about viral Reference Sequences, a collection of reference sequences for thousands of viral genomes.
- Virus Variation
An extension of the Influenza Virus Resource to other organisms, providing an interface to download sequence sets of selected viruses, analysis tools, including virus-specific BLAST pages, and genome annotation pipelines.
This site contains genome sequence and mapping data for organisms in Entrez Genome. The data are organized in directories for single species or groups of species. Mapping data are collected in the directory MapView and are organized by species. See the README file in the root directory and the README files in the species subdirectories for detailed information.
Contains directories for each genome that include available mapping data for current and previous builds of that genome.
This site contains all nucleotide and protein sequence records in the Reference Sequence (RefSeq) collection. The ""release"" directory contains the most current release of the complete collection, while data for selected organisms (such as human, mouse and rat) are available in separate directories. Data are available in FASTA and flat file formats. See the README file for details.
This site contains SKY-CGH data in ASN.1, XML and EasySKYCGH formats. See the skycghreadme.txt file for more information.
- FTP: Sequence Read Archive (SRA) Download Facility
This site contains next-generation sequencing data organized by the submitted sequencing project.
This site contains the trace chromatogram data organized by species. Data include chromatogram, quality scores, FASTA sequences from automatic base calls, and other ancillary information in tab-delimited text as well as XML formats. See the README file for details.
This site contains whole genome shotgun sequence data organized by the 4-digit project code. Data include GenBank and GenPept flat files, quality scores and summary statistics. See the README.genbank.wgs file for more information.
An online form that provides an interface for researchers, consortia and organizations to register their BioProjects. This serves as the starting point for the submission of genomic and genetic data for the study. The data does not need to be submitted at the time of BioProject registration.
- GenBank: tbl2asn
A command-line program that automates the creation of sequence records for submission to GenBank using many of the same functions as Sequin. It is used primarily for submission of complete genomes and large batches of sequences.
- Sequence Read Archive Submission
This link describes how submitters of SRA data can obtain a secure KOK体育官方网站 FTP site for their data, and also describes the allowed data formats and directory structures.
A single entry point for submitters to link to and find information about all of the data submission processes at KOK体育官方网站. Currently, this serves as an interface for the registration of BioProjects and BioSamples and submission of data for WGS and GTR. Future additions to this site are planned.
- Trace Archive Submission
This link describes how submitters of trace data can obtain a secure KOK体育官方网站 FTP site for their data, and also describes the allowed data formats and directory structures.
- 1000 Genomes Browser
An interactive graphical viewer that allows users to explore variant calls, genotype calls and supporting evidence (such as aligned sequence reads) that have been produced by the .
Performs a BLAST search for similar sequences from selected complete eukaryotic and prokaryotic genomes.
Performs a BLAST search of the genomic sequences in the RefSeqGene/LRG set. The default display provides ready navigation to review alignments in the Graphics display.
- Genome BLAST
This tool compares nucleotide or protein sequences to genomic sequence databases and calculates the statistical significance of matches using the Basic Local Alignment Search Tool (BLAST) algorithm.
- Genome Data Viewer (GDV)
A genome browser for interactive navigation of eukaryotic RefSeq genome assemblies with comprehensive inspection of gene, expression, variation and other annotations. GDV offers easy-to-load analytical track pre-configurations, a menu of data tracks for easy display and customization, and supports upload and analysis of user data. This browser also enables the production of displays for publishing.
- Genome Decoration Page
An online tool that assists in the production of journal quality figures of annotations on an ideogram or sequence representation of an assembly.
- Genome Remapping Service
KOK体育官方网站's Remap tool allows users to project annotation data and convert locations of features from one genomic assembly to another or to RefSeqGene sequences through a base by base analysis. Options are provided to adjust the stringency of remapping, and summary results are displayed on the web page. Full results can be downloaded for viewing in KOK体育官方网站's Genome Workbench graphical viewer, and annotation data for the remapped features, as well as summary data, is also available for download.
- Genome Workbench
An integrated application for viewing and analyzing sequence data. With Genome Workbench, you can view data in publically available sequence databases at KOK体育官方网站, and mix these data with your own data.
- Phenotype-Genotype Integrator (PheGenI)
Supports finding human phenotype/genotype relationships with queries by phenotype, chromosome location, gene, and SNP identifiers. Currently includes information from dbGaP, the NHGRI GWAS Catalog, and GTeX. Displays results on the genome, on sequence, or in tables for download.
A utility for computing alignment of proteins to genomic nucleotide sequence. It is based on a variation of the Needleman Wunsch global alignment algorithm and specifically accounts for introns and splice signals. Due to this algorithm, ProSplign is accurate in determining splice sites and tolerant to sequencing errors.
- Sequence Cytogenetic Conversion Service
- An online tool that converts sequence and cytogenetic coordinates for human, rat, mouse and fruit fly genomic assemblies.
- Sequence Viewer
Provides a configurable graphical display of a nucleotide or protein sequence and features that have been annotated on that sequence. In addition to use on KOK体育官方网站 sequence database pages, this viewer is available as an embeddable webpage component. Detailed documentation including an API Reference guide is available for developers wishing to embed the viewer in their own pages.
A utility for computing cDNA-to-Genomic sequence alignments. It is based on a variation of the Needleman-Wunsch global alignment algorithm and specifically accounts for introns and splice signals. Due to this algorithm, Splign is accurate in determining splice sites and tolerant to sequencing errors.
- Variation Viewer
- A genomic browser to search and view genomic variations listed in dbSNP, dbVar, and ClinVar databases. Searches can be performed using chromosomal location, gene symbol, phenotype, or variant IDs from dbSNP and dbVar. The browser enables exploration of results in a dynamic graphical sequence viewer with annotated tables of variations.
- Viral Genotyping Tool
This tool helps identify the genotype of a viral sequence. A window is slid along the query sequence and each window is compared by BLAST to each of the reference sequences for a particular virus.
- Submit data to KOK体育官方网站
- Submit sequence data to KOK体育官方网站
- Compare protein homologs between two microbial genomes
- Convert feature coordinates between genomic assemblies
- Display genomic annotation graphically
- Download the complete genome for an organism
- View/download features around an object or between two objects on a chromosome
- Find sequenced genomes, including those in progress, for a taxonomic group
- Determine conserved synteny between the genomes of two organisms
- Link from an object on a map to another resource