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Found 8 result(s)

NCBI Nucleotide

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The NCBI Nucleotide database collects sequences from such sources as GenBank, RefSeq, TPA, and PDB. Sequences collected relate to genome, gene, and transcript sequence data, and provide a foundation for research related to the biomedical field.

Satellog

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Satellog is a database to identify and dynamically prioritize repeats by using various characteristics, for example, repeat unit, repeat length percentile rank, class, period, total length, genomic coordinates, UniGene polymorphism profile, proximity to or presence within gene regions, such as CDS, UTR, location upstream.

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.

miRBase

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The miRBase database is a searchable database of published miRNA sequences and annotation. Each entry in the miRBase Sequence database represents a predicted hairpin portion of a miRNA transcript (termed mir in the database), with information on the location and sequence of the mature miRNA sequence (termed miR). Both hairpin and mature sequences are available for searching and browsing, and entries can also be retrieved by name, keyword, references and annotation. All sequence and annotation data are also available for download. The miRBase Registry provides miRNA gene hunters with unique names for novel miRNA genes prior to publication of results.

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.

UniGene

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<<<!!!<<< This repository is no longer available>>>!!!>>>. Although the web pages are no longer available, you will still be able to download the final UniGene builds as static content from the FTP site https://ftp.ncbi.nlm.nih.gov/repository/UniGene/. You will also be able to match UniGene cluster numbers to Gene records by searching Gene with UniGene cluster numbers. For best results, restrict to the “UniGene Cluster Number” field rather than all fields in Gene. For example, a search with Mm.2108[UniGene Cluster Number] finds the mouse transthyretin Gene record (Ttr). You can use the advanced search page https://www.ncbi.nlm.nih.gov/gene/advanced to help construct these searches. Keep in mind that the Gene record contains selected Reference Sequences and GenBank mRNA sequences rather than the larger set of expressed sequences in the UniGene cluster.

Kiezdeutschkorpus KiDKo

KiDKo

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The KiezDeutsch-Korpus (KiDKo) has been developed by project B6 (PI: Heike Wiese) of the collaborative research centre Information Structure (SFB 632) at the University of Potsdam from 2008 to 2015. KiDKo is a multi-modal digital corpus of spontaneous discourse data from informal, oral peer group situations in multi- and monoethnic speech communities. KiDKo contains audio data from self-recordings, with aligned transcriptions (i.e., at every point in a transcript, one can access the corresponding area in the audio file). The corpus provides parts-of-speech tags as well as an orthographically normalised layer (Rehbein & Schalowski 2013). Another annotation level provides information on syntactic chunks and topological fields. There are several complementary corpora: KiDKo/E (Einstellungen - "attitudes") captures spontaneous data from the public discussion on Kiezdeutsch: it assembles emails and readers' comments posted in reaction to media reports on Kiezdeutsch. By doing so, KiDKo/E provides data on language attitudes, language perceptions, and language ideologies, which became apparent in the context of the debate on Kiezdeutsch, but which frequently related to such broader domains as multilingualism, standard language, language prestige, and social class. KiDKo/LL ("Linguistic Landscape") assembles photos of written language productions in public space from the context of Kiezdeutsch, for instance love notes on walls, park benches, and playgrounds, graffiti in house entrances, and scribbled messages on toilet walls. Contains materials in following languages: Spanish, Italian, Greek, Kurdish, Swedish, French, Croatian, Arabic, Turkish. The corpus is available online via the Hamburger Zentrum für Sprachkorpora (HZSK) https://corpora.uni-hamburg.de/secure/annis-switch.php?instance=kidko .

AceView

AceView genes

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AceView provides a curated, comprehensive and non-redundant sequence representation of all public mRNA sequences (mRNAs from GenBank or RefSeq, and single pass cDNA sequences from dbEST and Trace). These experimental cDNA sequences are first co-aligned on the genome then clustered into a minimal number of alternative transcript variants and grouped into genes. Using exhaustively and with high quality standards the available cDNA sequences evidences the beauty and complexity of mammals’ transcriptome, and the relative simplicity of the nematode and plant transcriptomes. Genes are classified according to their inferred coding potential; many presumably non-coding genes are discovered. Genes are named by Entrez Gene names when available, else by AceView gene names, stable from release to release. Alternative features (promoters, introns and exons, polyadenylation signals) and coding potential, including motifs, domains, and homologies are annotated in depth; tissues where expression has been observed are listed in order of representation; diseases, phenotypes, pathways, functions, localization or interactions are annotated by mining selected sources, in particular PubMed, GAD and Entrez Gene, and also by performing manual annotation, especially in the worm. In this way, both the anatomy and physiology of the experimentally cDNA supported human, mouse and nematode genes are thoroughly annotated.