The whole genome assembly of Drosophila

  title={The whole genome assembly of Drosophila},
  author={Eugene Wimberly Myers},
  volume={287 5461},
  • E. Myers
  • Published 1 February 2000
  • Biology
  • Science
We report on the quality of a whole-genome assembly of Drosophila melanogaster and the nature of the computer algorithms that accomplished it. [] Key Result As such, this initial reconstruction of the Drosophila sequence should be of substantial value to the scientific community.

The genome sequence of Drosophila melanogaster.

The nucleotide sequence of nearly all of the approximately 120-megabase euchromatic portion of the Drosophila genome is determined using a whole-genome shotgun sequencing strategy supported by extensive clone-based sequence and a high-quality bacterial artificial chromosome physical map.

Y Chromosome and Other Heterochromatic Sequences of the Drosophila Melanogaster Genome: How Far can we go?

Methods are being expanded to make best use of all available clues to determine which unmapped contigs are associated with genes, including use of EST libraries, and, in the case of the Y chromosome, testing of male specific genes and reduced shotgun depth of relevant contigs.

Assembly of the working draft of the human genome with GigAssembler.

This work describes the algorithm used by GigAssembler, which produced the first publicly available assembly of the human genome, a working draft containing roughly 2.7 billion base pairs and covering an estimated 88% of the genome that has been used for several recent studies of the genomes.

The Drosophila melanogaster genome.

The current state of the Drosophila melanogaster genome sequence and its structural annotation is reviewed and some promising approaches that are being taken to achieve an initial functional annotation are summarized.

Whole-genome sequence assembly for mammalian genomes: Arachne 2.

Algorithmic adaptations to the whole-genome assembly program Arachne are described, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes.

A BAC-based physical map of the major autosomes of Drosophila melanogaster.

A bacterial artificial chromosome (BAC)-based physical map of chromosomes 2 and 3 of Drosophila melanogaster, which constitute 81% of the genome, is constructed to produce a map spanning the euchromatin.

Initial de novo Assemblies of the D. melanogaster genome using long-read PacBio sequencing

The level of completeness in the de novo assemblies presented here is unprecedented in a metazoan genome.

The Release 6 reference sequence of the Drosophila melanogaster genome.

An improved reference sequence of the single-copy and middle-repetitive regions of the genome is reported, produced using cytogenetic mapping to mitotic and polytene chromosomes, clone-based finishing and BAC fingerprint verification, ordering of scaffolds by alignment to cDNA sequences, incorporation of other map and sequence data, and validation by whole-genome optical restriction mapping.

Comparative genome assembly

A novel algorithm for comparative genome assembly that can accurately assemble a typical bacterial genome in less than four minutes on a standard desktop computer is described.

From first base: the sequence of the tip of the X chromosome of Drosophila melanogaster, a comparison of two sequencing strategies.

The sequence of a contiguous 2.63 Mb of DNA extending from the tip of the X chromosome of Drosophila melanogaster is presented and the insertion sites of P-elements from 111 mutant lines are determined, about half of which are in a position likely to affect the expression of novel predicted genes, thus representing a resource for subsequent functional genomic analysis.



Human whole-genome shotgun sequencing.

This article outlines an alternative approach to sequencing the human and other large genomes, which it is argued is less costly and more informative than the clone-by-clone approach.

The complete genome sequence of Escherichia coli K-12.

The 4,639,221-base pair sequence of Escherichia coli K-12 is presented and reveals ubiquitous as well as narrowly distributed gene families; many families of similar genes within E. coli are also evident.

Against a whole-genome shotgun.

It is argued here that the whole-genome shotgun proposed by Weber and Myers satisfies neither the high probability of success nor the decreased cost of any such approach.

Shotgun Sequencing of the Human Genome

The scientific rationale for the proposal and the business plan of the company are described, which aims to sequence the human genome four years faster and at lower cost than the government-backed Human Genome Project.

A new strategy for genome sequencing

This work has shown that there is a simpler strategy in which any number of laboratories can cooperate and the assumption that each region to be sequenced must first be mapped is wrong.

Basic local alignment search tool.

Gapped BLAST and PSI-BLAST: a new generation of protein database search programs.

A new criterion for triggering the extension of word hits, combined with a new heuristic for generating gapped alignments, yields a gapped BLAST program that runs at approximately three times the speed of the original.

During the first 9 months of development, when no significant amount of real data was available, we used a simulator called celsim

  • Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology

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  • Science
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