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Velvet: algorithms for de novo short read assembly using de Bruijn graphs.
Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies and is in close agreement with simulated results without read-pair information.
Initial sequencing and analysis of the human genome.
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.
A Draft Sequence of the Neandertal Genome
The genomic data suggest that Neandertals mixed with modern human ancestors some 120,000 years ago, leaving traces of Ne andertal DNA in contemporary humans, suggesting that gene flow from Neand Bertals into the ancestors of non-Africans occurred before the divergence of Eurasian groups from each other.
Automated generation of heuristics for biological sequence comparison
B bounded sparse dynamic programming (BSDP) is introduced to allow rapid implementation of heuristics approximating to many complex alignment models, and has been incorporated into the freely available sequence alignment program, exonerate.
Oases: robust de novo RNA-seq assembly across the dynamic range of expression levels
A software package named Oases designed to heuristically assemble RNA-seq reads in the absence of a reference genome, across a broad spectrum of expression values and in presence of alternative isoforms is presented.
GeneWise and Genomewise.
Two algorithms are presented, which predicts gene structure using similar protein sequences, and Genomewise, which provides a gene structure final parse across cDNA- and EST-defined spliced structure.
The Ensembl genome database project
The Ensembl (http://www.ensembl.org/) database project provides a bioinformatics framework to organise biology around the sequences of large genomes. It is a comprehensive source of stable automatic…
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.
Mouse genomic variation and its effect on phenotypes and gene regulation
These sequences provide a starting point for a new era in the functional analysis of a key model organism and show that the molecular nature of functional variants and their position relative to genes vary according to the effect size of the locus.
The genomic basis of adaptive evolution in threespine sticklebacks
A high-quality reference genome assembly for threespine stickleback fish is developed and it is indicated that reuse of globally shared standing genetic variation has an important role in repeated evolution of distinct marine and freshwater sticklebacks, and in the maintenance of divergent ecotypes during early stages of reproductive isolation.