Standards > model/format > bsg-s000232


ready GenBank Sequence Format

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General Information
"GenBank Sequence Format" is a standard, specialising in the fields described under "scope and data types", below. Until this entry is claimed, more information on this project can be found at http://www.bioperl.org/wiki/GenBank_sequence_format. This text was generated automatically. If you work on the project responsible for "GenBank Sequence Format" then please consider helping us by claiming this record and updating it appropriately.

Homepage http://www.bioperl.org/wiki/GenBank_sequence_format

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Record updated: Oct. 19, 2016, 9:22 p.m. by Madekale.


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Implementing Databases (27)
GenBank
GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. GenBank is part of the International Nucleotide Sequence Database Collaboration, which comprises the DNA DataBank of Japan (DDBJ), the European Molecular Biology Laboratory (EMBL), and GenBank at NCBI. These three organizations exchange data on a daily basis. The complete release notes for the current version of GenBank are available on the NCBI ftp site. A new release is made every two months. GenBank growth statistics for both the traditional GenBank divisions and the WGS division are available from each release.

Central Aspergillus Data REpository
This project aims to support the international Aspergillus research community by gathering all genomic information regarding this significant genus into one resource - The Central Aspergillus REsource (CADRE). CADRE facilitates visualisation and analyses of data using the Ensembl software suite. Much of our data has been extracted from Genbank and augmented with the consent of the original sequencing groups. This additional work has been carried out using both automated and manual efforts, with support from specific annotation projects and the general Aspergillus community.

CoryneRegNet 6.0 - Corynebacterial Regulation Network
Corynebacterial Regulation Network a reference database and analysis platform for corynebacterial transcription factors and gene regulatory networks.

Dragon Antimicrobial Peptide Database
Dragon Antimicrobial Peptide Database is a manually curated database of known and putative antimicrobial peptides (AMPs). It covers both prokaryotes and eukaryotes organisms.

The DNA Data Bank of Japan
Annotated collection of all publicly available nucleotide and protein sequences. In Japan, DDBJ Center internationally contributes as a member of INSDC to collect and to provide nucleotide sequence data with ENA/EBI in Europe and NCBI in USA. DDBJ collects sequence data mainly from Japanese researchers, as well as researchers in any other countries. Ninety-nine percent of INSD data from Japanese researchers are submitted through DDBJ.

EcoliWiki: A Wiki-based community resource for Escherichia coli
Community-based resource for the annotation of all non-pathogenic E. coli, its phages, plasmids, and mobile genetic elements.

FlyBase
Genetic, genomic and molecular information pertaining to the model organism Drosophila melanogaster and related sequences. This database also contains information relating to human disease models in Drosophila, the use of transgenic constructs containing sequence from other organisms in Drosophila, and information on where to buy Drosophila strains and constructs.

Integrative and Conjugative Elements in Bacteria
A web-based resource for integrative and conjugative elements (ICEs) found in bacteria. It collates available data from experimental and bioinformatics analyses, and literature, about known and putative ICEs in bacteria as a PostgreSQL-based database called ICEberg. This database contains detailed information on all archived ICEs and the genes carried by each entity, including unique identifiers, species details and hyperlink-paths to other public databases, like NCBI, UniprotKB and KEGG.

IMG/M: the integrated metagenome data management and comparative analysis system
Data management and analysis system for metagenomes

Minimotif Miner 3.0
A database of short functional motifs involved in posttranslational modifications, binding to other proteins, nucleic acids, or small molecules.

MIPModDB: A Central Resource for the Superfamily of Major Intrinsic Proteins
This is a database of comparative protein structure models of MIP (Major Intrinsic Protein) family of proteins. The nearly completed sets of MIPs have been identified from the completed genome sequence of organisms available at NCBI. The structural models of MIP proteins were created by defined protocol. The database aims to provide key information of MIPs in particular based on sequence as well as structures. This will further help to decipher the function of uncharacterized MIPs.

NONCODE
NONCODE is a database of noncoding RNAs (except tRNAs and rRNAs). This resource is a comprehensive collection and annotation of noncoding RNAs including details of long noncoding (lnc) RNAs. The database provides access to data on the relationships of lncRNAs to disease, conservation annotation, and high-quality datasets.

Group II introns database
Database for identification and cataloguing of group II introns. All bacterial introns listed in the main page are full-length and appear to be functional, based on intron RNA and IEP characteristics. The database names the full-length introns, and provides information on their boundaries, host genes, and secondary structures. In addition, the website provides tools for analysis that may be useful to researchers who encounter group II introns in DNA sequences.

Death Domain Database
Death Domain Database is a manually curated database of protein-protein interactions for Death Domain Superfamily.

SpliceDisease
The SpliceDisease database provides information linking RNA splicing to human disease, including the change of the nucleotide in the sequence, the location of the mutation on the gene, the reference Pubmed ID and detailed description for the relationship among gene mutations, splicing defects and diseases.

Virus Pathogen Database and Analysis Resource
The Virus Pathogen Database and Analysis Resource (ViPR) is an integrated repository of data and analysis tools for multiple virus families, supported by the National Institute of Allergy and Infectious Diseases (NIAID) Bioinformatics Resource Centers (BRC) program. ViPR captures various types of information, including sequence records, gene and protein annotations, 3D protein structures, immune epitope locations, clinical and surveillance metadata and novel data derived from comparative genomics analysis. The database is available without charge as a service to the virology research community to help facilitate the development of diagnostics, prophylactics and therapeutics for priority pathogens and other viruses.

Influenza Research Database
The Influenza Research Database (IRD) is a free, open, publicly-accessible resource funded by the U.S. National Institute of Allergy and Infectious Diseases through the Bioinformatics Resource Centers program. IRD provides a comprehensive, integrated database and analysis resource for influenza sequence, surveillance, and research data, including user-friendly interfaces for data retrieval, visualization, and comparative genomics analysis, together with personal login- protected ‘workbench’ spaces for saving data sets and analysis results. IRD integrates genomic, proteomic, immune epitope, and surveillance data from a variety of sources, including public databases, computational algorithms, external research groups, and the scientific literature.

autoSNPdb
Implemented the SNP discovery software autoSNP within a relational database to enable the efficient mining of the identified polymorphisms and the detailed interrogation of the data. AutoSNP was selected because it does not require sequence trace files and is thus applicable to a broader range of species and datasets.

Addgene
Addgene is a non-profit plasmid repository dedicated to helping scientists around the world share high-quality plasmids. Addgene are working with thousands of laboratories to assemble a high-quality library of published plasmids for use in research and discovery. By linking plasmids with articles, scientists can always find data related to the materials they request.

Plant Genome Network
PGN is a repository for plant EST sequence data located at Cornell. It comprises an analysis pipeline and a website, and presently contains mainly data from the Floral Genome Project.

Sol Genomics Network
The Sol Genomics Network (SGN) is a database and website dedicated to the genomic information of the Solanaceae family, which includes species such as tomato, potato, pepper, petunia and eggplant.

Influenza Virus Resource
Influenza Virus Resource presents data obtained from the NIAID Influenza Genome Sequencing Project as well as from GenBank, combined with tools for flu sequence analysis, annotation and submission to GenBank. In addition, it provides links to other resources that contain flu sequences, publications and general information about flu viruses.

Pseudomonas Genome DB
The Pseudomonas Genome Database is a resource for peer-reviewed, continually updated annotation for all Pseudomonas species. It includes gene and protein sequence information, as well as regulation and predicted function and annotation.

The Signaling Gateway
The Signaling Gateway provides information on mammalian proteins involved in cellular signaling.

A Systematic Annotation Package
ASAP is a relational database and web interface developed to store, update and distribute genome sequence data and gene expression data. It was designed to facilitate ongoing community annotation of genomes and to grow with genome projects as they move from the preliminary data stage through post-sequencing functional analysis.

dictyBase
A single-access database for the genome of four Dictyostelid species providing information on research, genome and annotations. There is also a repository of plasmids and strains held at the Dicty Stock Centre.

BCCM/LMBP Plasmid Collection
The BCCM/LMBP Plasmid Collection warrants the long-term storage and distribution of plasmids, microbial host strains and DNA libraries of fundamental, biotechnological, educational or general scientific importance. The focus is on the collection of recombinant plasmids that can replicate in a microbial host strain. BCCM/LMBP also accepts natural and genetically modified animal or human cell lines, including hybridomas, as well as other genetic material, in the safe deposit and patent deposit collections.

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