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  • References (28)
  • Cited By (1)
Published on Jan 1, 2002
Sung-bong Yang1
Estimated H-index: 1
3 Citations
Published on Jan 1, 1994 in Intelligent Systems in Molecular Biology
Pankaj K. Agarwal52
Estimated H-index: 52
David J. States32
Estimated H-index: 32
Over 3.6 million bases of DNA sequence from chromosome III of the C. eleganshave been determined. The availability of this extended region of contiguous sequence has allowed us to a~nalyze the nature and prevalence of repetitive sequences in the genome of a eukaryotic organism with a high gene density. We have assembled a Repeat Pattern Toolkit (RPT) to analyze the patterns of repeats occurring in DNA. The tools include identifying significant locM alignments (utilizing both two-way and three-wa...
28 Citations
Published on Aug 1, 2001in Genome Biology 13.21
Natalia Volfovsky15
Estimated H-index: 15
Brian J. Haas64
Estimated H-index: 64
Steven L. Salzberg118
Estimated H-index: 118
Background A computational system for analysis of the repetitive structure of genomic sequences is described. The method uses suffix trees to organize and search the input sequences; this data structure has been used previously for efficient computation of exact and degenerate repeats.
118 Citations Source Cite
Published on Aug 19, 2000 in Intelligent Systems in Molecular Biology
Stefan Kurtz30
Estimated H-index: 30
(Bielefeld University),
Enno Ohlebusch23
Estimated H-index: 23
+ 2 AuthorsRobert Giegerich35
Estimated H-index: 35
The repetitive structure of genomic DNA holds many secrets to be discovered. A systematic study of repetitive DNA on a genomic or inter-genomic scale requires extensive algorithmic support. The REPuter family of programs described herein was designed to serve as a fundamental tool in such studies. Efficient and complete detection of various types of repeats is provided together with an evaluation of significance, interactive visualization, and simple interfacing to other analysis programs.
50 Citations
Published on Mar 24, 2000in Science 41.06
Eugene W. Myers53
Estimated H-index: 53
(Celera Corporation),
Granger Sutton54
Estimated H-index: 54
(Celera Corporation)
+ 26 AuthorsKarin A. Remington17
Estimated H-index: 17
(Celera Corporation)
We report on the quality of a whole-genome assembly of Drosophila melanogaster and the nature of the computer algorithms that accomplished it. Three independent external data sources essentially agree with and support the assembly9s sequence and ordering of contigs across the euchromatic portion of the genome. In addition, there are isolated contigs that we believe represent nonrepetitive pockets within the heterochromatin of the centromeres. Comparison with a previously sequenced 2.9- megabase ...
1,157 Citations Source Cite
Itsik Pe'er38
Estimated H-index: 38
(Tel Aviv University),
Naama Arbili2
Estimated H-index: 2
(Tel Aviv University),
Ron Shamir61
Estimated H-index: 61
(Tel Aviv University)
Universal arrays contain all possible oligonucleotides of a certain length, typically 6–10 bases. They can determine in a single experiment all substrings of that length that occur along a target sequence. That information, also called the spectrum of the sequence, is not sufficient to uniquely reconstruct a sequence longer than a few hundred bases. We have devised a polynomial algorithm that reconstructs the sequence, given the spectrum and an additional reference sequence, homologous to the ta...
16 Citations Source Cite
Published on Jan 1, 1995in Journal of Computational Biology 1.19
Eugene W. Myers53
Estimated H-index: 53
ABSTRACT The fragment assembly problem is that of reconstructing a DNA sequence from a collection of randomly sampled fragments. Traditionally, the objective of this problem has been to produce the shortest string that contains all the fragments as substrings, but in the case of repetitive target sequences this objective produces answers that are overcompressed. In this paper, the problem is reformulated as one of finding a maximum-likelihood reconstruction with respect to the two-sided Kolmogor...
188 Citations Source Cite
Published on Apr 1, 2004in Genome Research 10.10
Guillaume Bourque37
Estimated H-index: 37
Pavel A. Pevzner77
Estimated H-index: 77
Glenn Tesler27
Estimated H-index: 27
Recent analysis of genome rearrangements in human and mouse genomes revealed evidence for more rearrangements than thought previously and shed light on previously unknown features of mammalian evolution, like breakpoint reuse and numerous microrearrangements. However, two-way analysis cannot reveal the genomic architecture of ancestral mammals or assign rearrangement events to different lineages. Thus, the “original synteny” problem introduced by Nadeau and Sankoff previously, remains unsolved, ...
204 Citations Source Cite
Published on Sep 1, 1992in Genomics 2.91
Xiaoqiu Huang23
Estimated H-index: 23
(Michigan Technological University)
An effective computer program for assembling DNA fragments, the contig assembly program (CAP), has been developed. In the CAP program, a filter is used to eliminate quickly fragment pairs that could not possibly overlap, a dynamic programming algorithm is applied to compute the maximal-scoring overlapping alignment between each remaining pair of fragments, and a simple greedy approach is employed to assemble fragments in order of alignment scores. To identify the true fragment overlaps, the dyna...
269 Citations Source Cite
Published on Jan 1, 1995in Journal of Computational Biology 1.19
Ramana M. Idury1
Estimated H-index: 1
Michael S. Waterman61
Estimated H-index: 61
ABSTRACT Since the advent of rapid DNA sequencing methods in 1976, scientists have had the problem of inferring DNA sequences from sequenced fragments. Shotgun sequencing is a well-established biological and computational method used in practice. Many conventional algorithms for shotgun sequencing are based on the notion of pairwise fragment overlap. While shotgun sequencing infers a DNA sequence given the sequences of overlapping fragments, a recent and complementary method, called sequencing b...
218 Citations Source Cite
View next paperDe novo repeat classification and fragment assembly