Tag: nucleotide

GenBank is the NIH genetic sequence database, an annotated collection of all publicly available DNA sequences. 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. G ...

dbSNP contains human single nucleotide variations, microsatellites, and small-scale insertions and deletions along with publication, population frequency, molecular consequence, and genomic and RefSeq mapping information for both common variations an ...

The Sequence Read Archive (SRA) stores raw sequencing data from the next generation of sequencing platforms Data submitted to SRA. It is organized using a metadata model consisting of six objects: study, sample, experiment, run, analysis and submissi ...

The Conserved Domain Database (CDD) brings together several collections of multiple sequence alignments representing conserved domains, including NCBI-curated domains, which use 3D-structure information to explicitly to define domain boundaries and p ...

ArrayExpress is a database of functional genomics experiments that can be queried and the data downloaded. It includes gene expression data from microarray and high throughput sequencing studies. Data is collected to MIAME and MINSEQE standards. Expe ...

The Saccharomyces Genome Database (SGD) provides comprehensive integrated biological information for the budding yeast Saccharomyces cerevisiae along with search and analysis tools to explore these data, enabling the discovery of functional relations ...

The European Nucleotide Archive (ENA) is a globally comprehensive data resource for nucleotide sequence, spanning raw data, alignments and assemblies, functional and taxonomic annotation and rich contextual data relating to sequenced samples and expe ...

PHI-Base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions. PHI-base catalogues experimentally verified pathogenicity, virulence and effector genes from fungal, Oomycete ...

The BioSamples database aggregates sample information for reference samples (e.g. Coriell Cell lines) and samples for which data exist in one of the EBI's assay databases such as ArrayExpress, the European Nucleotide Archive or PRIDE. It provides lin ...

The dbEST contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. NCBI is in the process of merging EST and GSS records into the Nucleotide database, and the process is e ...

An annotated collection of all publicly available nucleotide and protein sequences. DDBJ collects sequence data mainly from Japanese researchers, as well as researchers in other countries. DDBJ is part of the International Nucleotide Sequence Databas ...

The NCBI Probe Database is 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.

The Candida Genome Database (CGD) provides access to genomic sequence data and manually curated functional information about genes and proteins of the human pathogen Candida albicans. It collects gene names and aliases, and assigns gene ontology term ...

ScerTF is a database of position weight matrices (PWMs) for transcription factors in Saccharomyces species. It identifies a single matrix for each TF that best predicts in vivo data, providing metrics related to the performance of that matrix in accu ...

DNAmod is an open-source database (https://dnamod.hoffmanlab.org) that catalogues DNA modifications and provides a single source to learn about their properties. The database annotates the chemical properties and structures of all curated modified DN ...

MycoBank is a database created for the mycological community (as well as scientific community more generally) to document new mycological names, combinations and associated data (such as descriptions and illustrations ). Pairwise sequence alignments ...

GenBank Sequence Format (GenBank Flat File Format) consists of an annotation section and a sequence section. The start of the annotation section is marked by a line beginning with the word "LOCUS". The start of sequence section is marked by a line be ...

PANDIT is a collection of multiple sequence alignments and phylogenetic trees covering many common protein domains. It contains the seed protein sequence alignments from the Pfam-A (curated families) database; nucleotide sequence alignments derived f ...

DDBJ Sequence Read Archive (DRA) is an archive database for output data generated by next-generation sequencing machines including Roche 454 GS System®, Illumina Genome Analyzer®, Applied Biosystems SOLiD® System, and others. DRA is a member of the I ...

A curated database of mutations and polymorphisms associated with Lafora Progressive Myoclonus Epilepsy. The Lafora progressive myoclonus epilepsy mutation and polymorphism database is a collection of hand curated mutation and polymorphism data for t ...

The Abbreviations and Symbols for Nucleic Acids, Polynucleotides and their Constituents, created by the IIUPAC-IUB Commission on Biochemical Nomenclature, formalizes the naming scheme for simple nucleotides; nucleotide coenzymes and related substance ...