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The vertebrate genome annotation (Vega) database

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TLDR
The Vertebrate Genome Annotation (Vega) database was first made public in 2004 and now contains comprehensive annotation on 20 of the 24 human chromosomes, four whole mouse chromosomes and around 40% of the zebrafish Danio rerio genome.
Abstract
The Vertebrate Genome Annotation (Vega) database (http://vegasangeracuk) has been designed to be a community resource for browsing manual annotation of finished sequences from a variety of vertebrate genomes Its core database is based on an Ensembl-style schema, extended to incorporate curation-specific metadata In collaboration with the genome sequencing centres, Vega attempts to present consistent high-quality annotation of the published human chromosome sequences In addition, it is also possible to view various finished regions from other vertebrates, including mouse and zebrafish Vega displays only manually annotated gene structures built using transcriptional evidence, which can be examined in the browser Attempts have been made to standardize the annotation procedure across each vertebrate genome, which should aid comparative analysis of orthologues across the different finished regions

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Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses

TL;DR: It is found that lincRNA expression is strikingly tissue-specific compared with coding genes, and that l incRNAs are typically coexpressed with their neighboring genes, albeit to an extent similar to that of pairs of neighboring protein-coding genes.
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BioMart and Bioconductor: a powerful link between biological databases and microarray data analysis

TL;DR: The biomaRt package provides a tight integration of large, public or locally installed BioMart databases with data analysis in Bioconductor creating a powerful environment for biological data mining.
References
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Journal ArticleDOI

Initial sequencing and analysis of the human genome.

Eric S. Lander, +248 more
- 15 Feb 2001 - 
TL;DR: The results of an international collaboration to produce and make freely available a draft sequence of the human genome are reported and an initial analysis is presented, describing some of the insights that can be gleaned from the sequence.
Journal ArticleDOI

The Pfam protein families database

TL;DR: The definition and use of family-specific, manually curated gathering thresholds are explained and some of the features of domains of unknown function (also known as DUFs) are discussed, which constitute a rapidly growing class of families within Pfam.
Journal ArticleDOI

tRNAscan-SE: a program for improved detection of transfer RNA genes in genomic sequence.

TL;DR: A program is described, tRNAscan-SE, which identifies 99-100% of transfer RNA genes in DNA sequence while giving less than one false positive per 15 gigabases.
Journal ArticleDOI

The Human Genome Browser at UCSC

TL;DR: A mature web tool for rapid and reliable display of any requested portion of the genome at any scale, together with several dozen aligned annotation tracks, is provided at http://genome.ucsc.edu.
Journal ArticleDOI

Database resources of the National Center for Biotechnology Information

TL;DR: In addition to maintaining the GenBank(R) nucleic acid sequence database, the National Center for Biotechnology Information (NCBI) provides data analysis and retrieval resources for the data in GenBank and other biological data made available through NCBI’s website.
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Initial sequencing and analysis of the human genome.

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