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RECOMB
2000
Springer
10 years 2 months ago
A compression algorithm for DNA sequences and its applications in genome comparison
We present a lossless compression algorithm, GenCompress, for genetic sequences, based on searching for approximate repeats. Our algorithm achieves the best compression ratios for...
Xin Chen, Sam Kwong, Ming Li
GCB
2000
Springer
137views Biometrics» more  GCB 2000»
10 years 2 months ago
Detecting Sporadic Recombination in DNA Alignments with Hidden Markov Models
Conventional phylogenetic tree estimation methods assume that all sites in a DNA multiple alignment have the same evolutionary history. This assumption is violated in data sets fro...
Dirk Husmeier, Frank Wright
CSB
2004
IEEE
177views Bioinformatics» more  CSB 2004»
10 years 2 months ago
Compressed Pattern Matching in DNA Sequences
We propose derivative Boyer-Moore (d-BM), a new compressed pattern matching algorithm in DNA sequences. This algorithm is based on the BoyerMoore method, which is one of the most ...
Lei Chen, Shiyong Lu, Jeffrey L. Ram
HPDC
1994
IEEE
10 years 2 months ago
Design and Implementation of Parallel Algorithms for Gene-Finding
Finding genes unequivocally in DNA sequences is one of the key goals of the Human Genome project. The human genome is a 9 billion character long DNA sequence and is estimated to c...
James Puthukattukaran, Suresh Chalasani, Periannan...
VISUALIZATION
1996
IEEE
10 years 2 months ago
Flexible Information Visualization of Multivariate Data from Biological Sequence Similarity Searches
Information visualization faces challenges presented by the need to represent abstract data and the relationships within the data. Previously, we presented a system for visualizin...
Ed Huai-hsin Chi, John Riedl, Elizabeth Shoop, Joh...
VISUALIZATION
1998
IEEE
10 years 2 months ago
Supporting detail-in-context for the DNA representation, H-curves
This paper presents a tool for the visual exploration of DNA sequences represented as H-curves [7]. Although very long sequences can be plotted using H-curves, micro-features are ...
M. L. Lantin, M. Sheelagh T. Carpendale
CSB
2002
IEEE
221views Bioinformatics» more  CSB 2002»
10 years 3 months ago
DNA Sequence Compression Using the Burrows-Wheeler Transform
-- We investigate off-line dictionary oriented approaches to DNA sequence compression, based on the Burrows-Wheeler Transform (BWT). The preponderance of short repeating patterns i...
Donald A. Adjeroh, Yong Zhang, Amar Mukherjee, Mat...
SOFTCO
2004
Springer
10 years 4 months ago
MultiNNProm: A Multi-Classifier System for Finding Genes
The computational identification of genes in DNA sequences has become an issue of crucial importance due to the large number of DNA molecules being currently sequenced. We present ...
Romesh Ranawana, Vasile Palade
WCC
2005
Springer
130views Cryptology» more  WCC 2005»
10 years 4 months ago
On the Design of Codes for DNA Computing
In this paper, we describe a broad class of problems arising in the context of designing codes for DNA computing. We primarily focus on design considerations pertaining to the phen...
Olgica Milenkovic, Navin Kashyap
WABI
2005
Springer
110views Bioinformatics» more  WABI 2005»
10 years 4 months ago
Alignment of Tandem Repeats with Excision, Duplication, Substitution and Indels (EDSI)
Abstract. Traditional sequence comparison by alignment applies a mutation model comprising two events, substitutions and indels (insertions or deletions) of single positions (SI). ...
Michael Sammeth, Thomas Weniger, Dag Harmsen, Jens...
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