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Galaxy: a platform for interactive large-scale genome analysis.
An interactive system, Galaxy, that combines the power of existing genome annotation databases with a simple Web portal to enable users to search remote resources, combine data from independent queries, and visualize the results.
PipMaker--a web server for aligning two genomic DNA sequences.
PipMaker is appropriate for comparing genomic sequences from any two related species, although the types of information that can be inferred depend on the level of conservation and the time and divergence rate since the separation of the species.
Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project
Functional data from multiple, diverse experiments performed on a targeted 1% of the human genome as part of the pilot phase of the ENCODE Project are reported, providing convincing evidence that the genome is pervasively transcribed, such that the majority of its bases can be found in primary transcripts.
Human-mouse alignments with BLASTZ.
This work describes BLASTZ, an independent implementation of the Gapped BLAST algorithm specifically designed for aligning two long genomic sequences, and its modifications, the hardware environment on which it is run, and several empirical studies to validate its results.
Initial sequencing and comparative analysis of the mouse genome.
The results of an international collaboration to produce a high-quality draft sequence of the mouse genome are reported and an initial comparative analysis of the Mouse and human genomes is presented, describing some of the insights that can be gleaned from the two sequences.
The ENCODE (ENCyclopedia Of DNA Elements) Project
The ENCyclopedia Of DNA Elements (ENCODE) Project is organized as an international consortium of computational and laboratory-based scientists working to develop and apply high-throughput approaches for detecting all sequence elements that confer biological function.
Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution
A draft genome sequence of the red jungle fowl, Gallus gallus, provides a new perspective on vertebrate genome evolution, while also improving the annotation of mammalian genomes.
Genome sequence of the Brown Norway rat yields insights into mammalian evolution
This first comprehensive analysis of the genome sequence of the Brown Norway (BN) rat strain is reported, which is the third complete mammalian genome to be deciphered, and three-way comparisons with the human and mouse genomes resolve details of mammalian evolution.
An integrated encyclopedia of DNA elements in the human genome
Panel C shows several SNPs associated with Crohn’s disease and other inflammatory diseases that reside in a large gene desert on chromosome 5, along with some epigenetic features suggestive of function.
A comparative encyclopedia of DNA elements in the mouse genome
By comparing with the human genome, this work not only confirms substantial conservation in the newly annotated potential functional sequences, but also finds a large degree of divergence of sequences involved in transcriptional regulation, chromatin state and higher order chromatin organization.