Results 1 - 10 of 2,570

ARACHNE: a whole-genome shotgun assembler

by Serafim Batzoglou, David B. Jaffe, Ken Stanley, Jonathan Butler, Sante Gnerre, Evan Mauceli, Bonnie Berger, Jill P. Mesirov, Eric S - Genome Res , 2002
"... We describe a new computer system, called ARACHNE, for assembling genome sequence using paired-end whole-genome shotgun reads. ARACHNE has several key features, including an efficient and sensitive procedure for finding read overlaps, a procedure for scoring overlaps that achieves high accuracy by c ..."
Abstract - Cited by 177 (7 self) - Add to MetaCart
We describe a new computer system, called ARACHNE, for assembling genome sequence using paired-end whole-genome shotgun reads. ARACHNE has several key features, including an efficient and sensitive procedure for finding read overlaps, a procedure for scoring overlaps that achieves high accuracy

Whole-Genome Sequence Assembly for Mammalian Genomes: Arachne 2

by David B. Jaffe, Jonathan Butler, Sante Gnerre, Evan Mauceli, Kerstin Lindblad-toh, Jill P. Mesirov, Michael C. Zody, Eric S. Lander
"... We previously described the whole-genome assembly program Arachne, presenting assemblies of simulated data for small to mid-sized genomes. Here we describe algorithmic adaptations to the program, allowing for assembly of mammalian-size genomes, and also improving the assembly of smaller genomes. Thr ..."
Abstract - Cited by 68 (2 self) - Add to MetaCart
are described in (Mouse Genome Sequencing Consortium 2002). In the whole-genome shotgun method of genome sequencing, as presently practiced, the entire genome is sheared to specified approximate sizes (generally chosen from the range 2–200 kb), yielding random fragments (called inserts), whose ends can

Assembly of protein tertiary structures from fragments with similar local sequences using simulated annealing and Bayesian scoring functions

by Kim T. Simons, Charles Kooperberg, Enoch Huang, David Baker - J. MOL. BIOL , 1997
"... We explore the ability of a simple simulated annealing procedure to assemble native-like structures from fragments of unrelated protein structures with similar local sequences using Bayesian scoring functions. Environment and residue pair specific contributions to the scoring functions appear as the ..."
Abstract - Cited by 393 (70 self) - Add to MetaCart
We explore the ability of a simple simulated annealing procedure to assemble native-like structures from fragments of unrelated protein structures with similar local sequences using Bayesian scoring functions. Environment and residue pair specific contributions to the scoring functions appear

Whole-genome sequencing and assembly with highthroughput, short read technologies

by Andreas Sundquist, Mostafa Ronaghi, Haixu Tang, Pavel Pevzner, Serafim Batzoglou - PLoS ONE , 2007
"... While recently developed short-read sequencing technologies may dramatically reduce the sequencing cost and eventually achieve the $1000 goal for re-sequencing, their limitations prevent the de novo sequencing of eukaryotic genomes with the standard shotgun sequencing protocol. We present SHRAP (SHo ..."
Abstract - Cited by 24 (1 self) - Add to MetaCart
. melanogaster and the entire human genome, our clone-ordering method produces accurate maps, thereby localizing fragment assembly and enabling the parallelization of the subsequent steps of our pipeline. Thus, we have demonstrated that truly inexpensive de novo sequencing of mammalian

Research Heterochromatic sequences in a Drosophila whole-genome shotgun assembly

by Roger A Hoskins, Christopher D Smith, Joseph W Carlson, A Bernardo, Aaron Halpern, Joshua S Kaminker, Cameron Kennedy, J Mungall, Beth A Sullivan, Granger G Sutton, Jiro C Yasuhara, Barbara T Wakimoto, Eugene W Myers, Susan E Celniker, Gerald M, Gary H Karpen , 2002
"... Background: Most eukaryotic genomes include a substantial repeat-rich fraction termed heterochromatin, which is concentrated in centric and telomeric regions. The repetitive nature of heterochromatic sequence makes it difficult to assemble and analyze. To better understand the heterochromatic compon ..."
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component of the Drosophila melanogaster genome, we characterized and annotated portions of a whole-genome shotgun sequence assembly. Results: WGS3, an improved whole-genome shotgun assembly, includes 20.7 Mb of draft-quality sequence not represented in the Release 3 sequence spanning the euchromatin. We

Whole-Genome Sequencing: Ready

by For Prime Time, David T. Miller, Ahmed A. Alfares
"... Rapid technological advances in DNA sequencing are facilitating the perception that whole-genome sequencing (WGS) will soon be available as a routine clinical diagnostic—and predictive—test. Current clinical testing is typically diagnostic, focusing on sin-gle genes or small gene panels, identifying ..."
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Rapid technological advances in DNA sequencing are facilitating the perception that whole-genome sequencing (WGS) will soon be available as a routine clinical diagnostic—and predictive—test. Current clinical testing is typically diagnostic, focusing on sin-gle genes or small gene panels

Human whole-genome shotgun sequencing

by James L. Weber, Eugene W. Myers - Genome Research , 1997
"... Large-scale sequencing of the human genome is now under way (Boguski et al. 1996; Marshall and Pennisi 1996). Although at the beginning of the Genome Project, many doubted the scientific value of sequencing the entire human genome, these doubts have evaporated almost entirely (Gibbs 1995; Olson 1995 ..."
Abstract - Cited by 40 (2 self) - Add to MetaCart
Escherichia coli clones, followed by complete sequencing of these clones one at a time. In this article, we outline an alternative approach to sequencing the human and other large genomes, which we argue is less costly and more informative than the clone-by-clone approach. A Plan for Human Whole-Genome

Whole-genome validation of high-information-content fingerprinting

by William M. Nelson, Arvind K. Bharti, Fusheng Wei, Galina Fuks, Hyeran Kim, Rod A. Wing, Joachim Messing, Carol Soderlund - Plant Physiol , 2005
"... Fluorescent-based high-information-content fingerprinting (HICF) techniques have recently been developed for physical mapping. These techniques make use of automated capillary DNA sequencing instruments to enable both high-resolution and high-throughput fingerprinting. In this article, we report the ..."
Abstract - Cited by 10 (1 self) - Add to MetaCart
as previously used for the whole-genome agarose FPC map, providing a unique opportunity for direct comparison of the agarose and HICF methods; as a result, it was found that HICF has substantially greater sensitivity in forming contigs. An improved assembly procedure is also described that uses automatic end

Sequencing technologies - the next generation.

by Michael L Metzker , Michael L Metzker - Nature Reviews , 2010
"... Abstract | Demand has never been greater for revolutionary technologies that deliver fast, inexpensive and accurate genome information. This challenge has catalysed the development of next-generation sequencing (NGS) technologies. The inexpensive production of large volumes of sequence data is the ..."
Abstract - Cited by 286 (2 self) - Add to MetaCart
is the primary advantage over conventional methods. Here, I present a technical review of template preparation, sequencing and imaging, genome alignment and assembly approaches, and recent advances in current and near-term commercially available NGS instruments. I also outline the broad range of applications

Bioinformatics Whole-Genome Validation of High-Information-Content

by William M. Nelson, Arvindk. Bharti, Fusheng Wei, Galina Fuks, Hyeran Kim, Rod A. Wing, Joachim Messing, Carol Soderlund
"... Fluorescent-based high-information-content fingerprinting (HICF) techniques have recently been developed for physical mapping. These techniques make use of automated capillary DNA sequencing instruments to enable both high-resolution and high-throughput fingerprinting. In this article, we report the ..."
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as previously used for the whole-genome agarose FPC map, providing a unique opportunity for direct comparison of the agarose and HICF methods; as a result, it was found that HICF has substantially greater sensitivity in forming contigs. An improved assembly procedure is also described that uses automatic end
Results 1 - 10 of 2,570