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Found 30 result(s)

BAliBASE

Benchmark Alignment dataBASE

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A collection of high quality multiple sequence alignments for objective, comparative studies of alignment algorithms. The alignments are constructed based on 3D structure superposition and manually refined to ensure alignment of important functional residues. A number of subsets are defined covering many of the most important problems encountered when aligning real sets of proteins. It is specifically designed to serve as an evaluation resource to address all the problems encountered when aligning complete sequences. The first release provided sets of reference alignments dealing with the problems of high variability, unequal repartition and large N/C-terminal extensions and internal insertions. Version 2.0 of the database incorporates three new reference sets of alignments containing structural repeats, trans-membrane sequences and circular permutations to evaluate the accuracy of detection/prediction and alignment of these complex sequences. Within the resource, users can look at a list of all the alignments, download the whole database by ftp, get the "c" program to compare a test alignment with the BAliBASE reference (The source code for the program is freely available), or look at the results of a comparison study of several multiple alignment programs, using BAliBASE reference sets.

Organelle Genome Megasequencing Program

OGMP

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The Organelle Genome Megasequencing Program (OGMP) provides mitochondrial, chloroplast, and mitochondrial plasmid genome data. OGMP tools allow direct comparison of OGMP and NCBI validated records. Includes GOBASE, a taxonomically broad organelle genome database that organizes and integrates diverse data related to mitochondria and chloroplasts.

FungiDB

The Fungal and Oomycete Genomics Resource

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FungiDB belongs to the EuPathDB family of databases and is an integrated genomic and functional genomic database for the kingdom Fungi. FungiDB was first released in early 2011 as a collaborative project between EuPathDB and the group of Jason Stajich (University of California, Riverside). At the end of 2015, FungiDB was integrated into the EuPathDB bioinformatic resource center. FungiDB integrates whole genome sequence and annotation and also includes experimental and environmental isolate sequence data. The database includes comparative genomics, analysis of gene expression, and supplemental bioinformatics analyses and a web interface for data-mining.

NCBI Structure

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The Structure database provides three-dimensional structures of macromolecules for a variety of research purposes and allows the user to retrieve structures for specific molecule types as well as structures for genes and proteins of interest. Three main databases comprise Structure-The Molecular Modeling Database; Conserved Domains and Protein Classification; and the BioSystems Database. Structure also links to the PubChem databases to connect biological activity data to the macromolecular structures. Users can locate structural templates for proteins and interactively view structures and sequence data to closely examine sequence-structure relationships.

OrtholugeDB

The Ortholog Database

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OrtholugeDB contains Ortholuge-based orthology predictions for completely sequenced bacterial and archaeal genomes. It is also a resource for reciprocal best BLAST-based ortholog predictions, in-paralog predictions (recently duplicated genes) and ortholog groups in Bacteria and Archaea. The Ortholuge method improves the specificity of high-throughput orthology prediction.

GeneCards

The Human Gene Database

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GeneCards is a searchable, integrative database that provides comprehensive, user-friendly information on all annotated and predicted human genes. It automatically integrates gene-centric data from ~125 web sources, including genomic, transcriptomic, proteomic, genetic, clinical and functional information.

cisRED

Databases of genome-wide regulatory module and element predictions

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<<<!!!<<< This repository is no longer available. >>>!!!>>>

Mammalian Transcriptomic Database

MTD

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MTD is focused on mammalian transcriptomes with a current version that contains data from humans, mice, rats and pigs. Regarding the core features, the MTD browses genes based on their neighboring genomic coordinates or joint KEGG pathway and provides expression information on exons, transcripts, and genes by integrating them into a genome browser. We developed a novel nomenclature for each transcript that considers its genomic position and transcriptional features.

European Variation Archive

EVA

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The European Variation Archive is an open-access database of all types of genetic variation data from all species. The EVA provides access to highly detailed, granular, raw variant data from human, with other species to follow. As of September 2017, EMBL-EBI will maintain reliable accessions for non-human genetic variation data through the European Variation Archive (EVA). NCBI's dbSNP database will continue to maintain stable identifiers for human genetic variation data only. This change will enable a more rapid turnaround for data sharing in this burgeoning field.

EcoCyc Database

EcoCyc E. coli Database

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EcoCyc is a scientific database for the bacterium Escherichia coli K-12 MG1655. The EcoCyc project performs literature-based curation of the entire genome, and of transcriptional regulation, transporters, and metabolic pathways.

IMGT/HLA Database

IPD-IMGT/HLA

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The IPD-IMGT/HLA Database provides a specialist database for sequences of the human major histocompatibility complex (MHC) and includes the official sequences named by the WHO Nomenclature Committee For Factors of the HLA System. The IPD-IMGT/HLA Database is part of the international ImMunoGeneTics project (IMGT). The database uses the 2010 naming convention for HLA alleles in all tools herein. To aid in the adoption of the new nomenclature, all search tools can be used with both the current and pre-2010 allele designations. The pre-2010 nomenclature designations are only used where older reports or outputs have been made available for download.

European Nucleotide Archive

ENA

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The European Nucleotide Archive (ENA) captures and presents information relating to experimental workflows that are based around nucleotide sequencing. A typical workflow includes the isolation and preparation of material for sequencing, a run of a sequencing machine in which sequencing data are produced and a subsequent bioinformatic analysis pipeline. ENA records this information in a data model that covers input information (sample, experimental setup, machine configuration), output machine data (sequence traces, reads and quality scores) and interpreted information (assembly, mapping, functional annotation). Data arrive at ENA from a variety of sources. These include submissions of raw data, assembled sequences and annotation from small-scale sequencing efforts, data provision from the major European sequencing centres and routine and comprehensive exchange with our partners in the International Nucleotide Sequence Database Collaboration (INSDC). Provision of nucleotide sequence data to ENA or its INSDC partners has become a central and mandatory step in the dissemination of research findings to the scientific community. ENA works with publishers of scientific literature and funding bodies to ensure compliance with these principles and to provide optimal submission systems and data access tools that work seamlessly with the published literature.

BioModels

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BioModels is a repository of mathematical models of biological and biomedical systems. It hosts a vast selection of existing literature-based physiologically and pharmaceutically relevant mechanistic models in standard formats. Our mission is to provide the systems modelling community with reproducible, high-quality, freely-accessible models published in the scientific literature.

J. Craig Venter Institute

JCVI

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JCVI is a world leader in genomic research. The Institute studies the societal implications of genomics in addition to genomics itself. The Institute's research involves genomic medicine; environmental genomic analysis; clean energy; synthetic biology; and ethics, law, and economics.

AnimalGenome.ORG

BioMart AnimalGenome.ORG

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This is a animal and human genome database that uses the BioMart software.

MetaCyc

Metabolic Pathway Database

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MetaCyc is a curated database of experimentally elucidated metabolic pathways from all domains of life. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated metabolites, reactions, enzymes, and genes. The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. MetaCyc applications include: Online encyclopedia of metabolism, Prediction of metabolic pathways in sequenced genomes, Support metabolic engineering via enzyme database, Metabolite database aids. metabolomics research.

NCBI Third Party Annotation

TPA

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TPA is a database that contains sequences built from the existing primary sequence data in GenBank. TPA records are retrieved through the Nucleotide Database and feature information on the sequence, how it was cataloged, and proper way to cite the sequence information.

Barcode of Life Data Systems

BOLD Systems

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The Barcode of Life Data Systems (BOLD) provides DNA barcode data. BOLD's online workbench supports data validation, annotation, and publication for specimen, distributional, and molecular data. The platform consists of four main modules: a data portal, a database of barcode clusters, an educational portal, and a data collection workbench. BOLD is the go-to site for DNA-based identification. As the central informatics platform for DNA barcoding, BOLD plays a crucial role in assimilating and organizing data gathered by the international barcode research community. Two iBOL (International Barcode of Life) Working Groups are supporting the ongoing development of BOLD.

RESID Database of Protein Modifications

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The RESID Database of Protein Modifications is a comprehensive collection of annotations and structures for protein modifications including amino-terminal, carboxyl-terminal and peptide chain cross-link post-translational modifications.

NAGRP Blast Center

National Animal Genome Research Program Blast Center

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NAGRP Blast Center aggregates various sequence databases and makes them accessible via its website.

NCBI PopSet

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NCBI PopSet collects DNA sequences to analyze the ways that populations are related by evolution. Such sequences indicate if populations originate from different members of the same species or from organisms of different species entirely.

The Global Proteome Machine

GPM

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The Global Proteome Machine (GPM) is a protein identification database. This data repository allows users to post and compare results. GPM's data is provided by contributors like The Informatics Factory, University of Michigan, and Pacific Northwestern National Laboratories. The GPM searchable databases are: GPMDB, pSYT, SNAP, MRM, PEPTIDE and HOT.

DRYAD

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Dryad is an open data publishing platform and a community committed to the open availability and routine re-use of all research data. We publish data in any format and any discipline. All Dryad data undergoes a curation process and is published under a CC0 waiver to promote reuse.

caArray

Array Data Management System

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>>>!!!<<< caArray Retirement Announcement >>>!!!<<< The National Cancer Institute (NCI) Center for Biomedical Informatics and Information Technology (CBIIT) instance of the caArray database was retired on March 31st, 2015. All publicly-accessible caArray data and annotations will be archived and will remain available via FTP download https://wiki.nci.nih.gov/x/UYHeDQ and is also available at GEO http://www.ncbi.nlm.nih.gov/geo/ . >>>!!!<<< While NCI will not be able to provide technical support for the caArray software after the retirement, the source code is available on GitHub https://github.com/NCIP/caarray , and we encourage continued community development. Molecular Analysis of Brain Neoplasia (Rembrandt fine-00037) gene expression data has been loaded into ArrayExpress: http://www.ebi.ac.uk/arrayexpress/experiments/E-MTAB-3073 >>>!!!<<< caArray is an open-source, web and programmatically accessible microarray data management system that supports the annotation of microarray data using MAGE-TAB and web-based forms. Data and annotations may be kept private to the owner, shared with user-defined collaboration groups, or made public. The NCI instance of caArray hosts many cancer-related public datasets available for download.

INTEGRALL

The Integron Database

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INTEGRALL is a web-based platform dedicated to compile information on integrons and designed to organize all the data available for these genetic structures. INTEGRALL provides a public genetic repository for sequence data and nomenclature and offers to scientists an easy and interactive access to integron's DNA sequences, their molecular arrangements as well as their genetic contexts.