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Found 7 result(s)

Expressed Sequence Tags database

dbEST

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dbEST is a division of GenBank that contains sequence data and other information on "single-pass" cDNA sequences, or "Expressed Sequence Tags", from a number of organisms. Expressed Sequence Tags (ESTs) are short (usually about 300-500 bp), single-pass sequence reads from mRNA (cDNA). Typically they are produced in large batches. They represent a snapshot of genes expressed in a given tissue and/or at a given developmental stage. They are tags (some coding, others not) of expression for a given cDNA library. Most EST projects develop large numbers of sequences. These are commonly submitted to GenBank and dbEST as batches of dozens to thousands of entries, with a great deal of redundancy in the citation, submitter and library information. To improve the efficiency of the submission process for this type of data, we have designed a special streamlined submission process and data format. dbEST also includes sequences that are longer than the traditional ESTs, or are produced as single sequences or in small batches. Among these sequences are products of differential display experiments and RACE experiments. The thing that these sequences have in common with traditional ESTs, regardless of length, quality, or quantity, is that there is little information that can be annotated in the record. If a sequence is later characterized and annotated with biological features such as a coding region, 5'UTR, or 3'UTR, it should be submitted through the regular GenBank submissions procedure (via BankIt or Sequin), even if part of the sequence is already in dbEST. dbEST is reserved for single-pass reads. Assembled sequences should not be submitted to dbEST. GenBank will accept assembled EST submissions for the forthcoming TSA (Transcriptome Shotgun Assembly) division. The individual reads which make up the assembly should be submitted to dbEST, the Trace archive or the Short Read Archive (SRA) prior to the submission of the assemblies.

IntAct

IntAct Molecular Interaction Database

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IntAct provides a freely available, open source database system and analysis tools for molecular interaction data. All interactions are derived from literature curation or direct user submissions and are freely available.

Database of Interacting Proteins

DIP

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The DIP database catalogs experimentally determined interactions between proteins. It combines information from a variety of sources to create a single, consistent set of protein-protein interactions. The data stored within the DIP database were curated, both, manually by expert curators and also automatically using computational approaches that utilize the the knowledge about the protein-protein interaction networks extracted from the most reliable, core subset of the DIP data. Please, check the reference page to find articles describing the DIP database in greater detail. The Database of Ligand-Receptor Partners (DLRP) is a subset of DIP (Database of Interacting Proteins). The DLRP is a database of protein ligand and protein receptor pairs that are known to interact with each other. By interact we mean that the ligand and receptor are members of a ligand-receptor complex and, unless otherwise noted, transduce a signal. In some instances the ligand and/or receptor may form a heterocomplex with other ligands/receptors in order to be functional. We have entered the majority of interactions in DLRP as full DIP entries, with links to references and additional information

Brain-CODE

Brain-Centre for Ontario Data Exploration

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Brain-CODE is a large-scale informatics platform that manages the acquisition and storage of multidimensional data collected from participants with a variety of brain disorders.

IMGT/GENE-DB

ImMunoGeneTics / Gene-DB

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IMGT/GENE-DB is the IMGT genome database for IG and TR genes from human, mouse and other vertebrates. IMGT/GENE-DB provides a full characterization of the genes and of their alleles: IMGT gene name and definition, chromosomal localization, number of alleles, and for each allele, the IMGT allele functionality, and the IMGT reference sequences and other sequences from the literature. IMGT/GENE-DB allele reference sequences are available in FASTA format (nucleotide and amino acid sequences with IMGT gaps according to the IMGT unique numbering, or without gaps).

database of Sequence Tagged Sites

dbSTS

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<<<!!!<<< The page is no longer available. This database was already retired, and on this page users could find information on how to search and use these sequences. dbSTS was an NCBI resource that contained sequence data for short genomic landmark sequences or Sequence Tagged Sites. STS sequences are incorporated into the STS Division of GenBank. >>>!!!>>>

ALEXA

ALEXA-A

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ALEXA is a microarray design platform for 'alternative expression analysis'. This platform facilitates the design of expression arrays for analysis of mRNA isoforms generated from a single locus by the use of alternative transcription initiation, splicing and polyadenylation sites. We use the term 'ALEXA' to describe a collection of novel genomic methods for 'alternative expression' analysis. 'Alternative expression' refers to the identification and quantification of alternative mRNA transcripts produced by alternative transcript initiation, alternative splicing and alternative polyadenylation. This website provides supplementary materials, source code and other downloads for recent publications describing our studies of alternative expression (AE). Most recently we have developed a method, 'ALEXA-Seq' and associated resources for alternative expression analysis by massively parallel RNA sequencing.