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APPROXIMATE MATCHING USING INTERVAL JUMPING SEARCHING ALGORITHMS FOR DNA SEQUENCES1

Published on Jan 1, 2004
Jia-Han Chu , Wei-Yuan Chang + 3 AuthorsHao Teng Chang13
Estimated H-index: 13
Abstract
The present invention, by improving the silicon surface/bulk micromachining technology using two steps of silicon etch mask patterning and four steps of silicon etching, fabricates a structure which has vertically offset electrodes and consequently fabricates an electrostatic vertical and torsional actuator using one single-crystalline silicon wafer. According to the method of the present invention, the problems of the prior art that used a number of silicon wafers and single/double SOI wafers, or combining of these wafers with additional deposited poly-crystalline silicon films, may be resolved.
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References8
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Published on Oct 1, 2001in Genome Research 10.10
Zemin Ning36
Estimated H-index: 36
(Wellcome Trust),
Anthony J. Cox2
Estimated H-index: 2
(Wellcome Trust),
James C. Mullikin72
Estimated H-index: 72
(Wellcome Trust)
We describe an algorithm, SSAHA (Sequence Search and Alignment by Hashing Algorithm), for performing fast searches on databases containing multiple gigabases of DNA. Sequences in the database are preprocessed by breaking them into consecutive k-tuples of k contiguous bases and then using a hash table to store the position of each occurrence of each k-tuple. Searching for a query sequence in the database is done by obtaining from the hash table the “hits” for each k-tuple in the query sequence an...
843 Citations Source Cite
Published on Aug 1, 2001in Genome Biology 13.21
Natalia Volfovsky16
Estimated H-index: 16
,
Brian J. Haas62
Estimated H-index: 62
,
Steven L. Salzberg120
Estimated H-index: 120
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.
120 Citations Source Cite
Published on Jul 1, 2001in Nature Reviews Genetics 41.47
Lincoln Stein84
Estimated H-index: 84
(Cold Spring Harbor Laboratory)
Now that many genome sequences are available, attention is shifting towards developing and improving approaches for genome annotation. Genome annotation can be classified into three levels: the nucleotide, protein and process levels. Gene finding is a chief aspect of nucleotide-level annotation. For complex genomes, the most successful methods use a combination of ab initio gene prediction and sequence comparison with expressed sequence databases and other organisms. Nucleotide-level annotation ...
253 Citations Source Cite
Published on Oct 1, 2000in Bioinformatics 5.48
Pierre Baldi82
Estimated H-index: 82
,
Pierre-François Baisnée3
Estimated H-index: 3
Motivation: DNA structure plays an important role in a variety of biological processes. Different di- and trinucleotide scales have been proposed to capture various aspects of DNA structure including base stacking energy, propeller twist angle, protein deformability, bendability, and position preference. Yet, a general framework for the computational analysis and prediction of DNA structure is still lacking. Such a framework should in particular address the following issues: (1) construction of ...
44 Citations Source Cite
Published on May 1, 1999in Journal of the ACM 1.74
Gene Myers13
Estimated H-index: 13
(University of Arizona)
The approximate string matching problem is to find all locations at which a query of length m matches a substring of a text of length n with k -or-fewer differences. Simple and practical bit-vector algorithms have been designed for this problem, most notably the one used in agrep . These algorithms compute a bit representation of the current state-set of the k -difference automaton for the query, and asymptotically run in either O ( nm/w ) or O ( nm log s/ w ) time where w is the word size of th...
296 Citations Source Cite
Published on Jun 1, 1995in The FASEB Journal 5.59
D Lohr1
Estimated H-index: 1
(Arizona State University),
P Venkov1
Estimated H-index: 1
(Arizona State University),
J Zlatanova1
Estimated H-index: 1
(Arizona State University)
Regulation of the GAL structural genes in the yeast Saccharomyces cerevisiae is implemented by the products of GAL-specific (GAL4, GAL80, GAL3) and general (GAL11, SWI1, 2, 3, SNF5, 6, numerous glucose repression) genes. Recent work has 1) yielded significant new insights on the DNA binding and transcription activation/Gal80 protein binding functions of the Gal4 activator protein, 2) described the characterization of purified Gal4 protein-Gal80 protein complexes, 3) deconvoluted the multiple and...
325 Citations Source Cite
Published on Sep 9, 1991
Petteri Jokinen2
Estimated H-index: 2
(University of Helsinki),
Esko Ukkonen40
Estimated H-index: 40
(University of Helsinki)
The problem of finding all approximate occurrences P′ of a pattern string P in a text string T such that the edit distance between P and P′ is ≤k is considered. We concentrate on a scheme in which T is first preprocessed to make the subsequent searches with different P fast. Two preprocessing methods and the corresponding search algorithms are described. The first is based suffix automata and is applicable for edit distances with general edit operation costs. The second is a special design for u...
141 Citations Source Cite
Published on Apr 1, 1985in Cell 31.40
Edward Giniger3
Estimated H-index: 3
(Harvard University),
Susan M. Varnum1
Estimated H-index: 1
(Harvard University),
Mark Ptashne79
Estimated H-index: 79
(Harvard University)
Abstract We show by the following series of experiments that the yeast positive regulatory protein GAL4 binds to four sites in the upstream activating sequence UAS G to activate transcription of the adjacent GAL1 and GAL10 genes. GAL4 protein expressed in E. coli protected guanine residues in UAS G from methylation by dimethyl sulfate. The same set of protections was seen in vivo in yeast and depended on the GAL4 + allele. This protection pattern is consistent with the idea that GAL4 protein bin...
480 Citations Source Cite
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