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WABI
2001
Springer
112views Bioinformatics» more  WABI 2001»
15 years 7 months ago
Finding an Optimal Inversion Median: Experimental Results
We derive a branch-and-bound algorithm to find an optimal inversion median of three signed permutations. The algorithm prunes to manageable size an extremely large search tree usi...
Adam C. Siepel, Bernard M. E. Moret
BIBM
2009
IEEE
118views Bioinformatics» more  BIBM 2009»
15 years 7 months ago
Inexact Local Alignment Search over Suffix Arrays
We describe an algorithm for finding approximate seeds for DNA homology searches. In contrast to previous algorithms that use exact or spaced seeds, our approximate seeds may conta...
Mohammadreza Ghodsi, Mihai Pop
DNA
2007
Springer
106views Bioinformatics» more  DNA 2007»
15 years 7 months ago
Hardware Acceleration for Thermodynamic Constrained DNA Code Generation
Reliable DNA computing requires a large pool of oligonucleotides that do not produce cross-hybridize. In this paper, we present a transformed algorithm to calculate the maximum wei...
Qinru Qiu, Prakash Mukre, Morgan Bishop, Daniel J....
BIBE
2004
IEEE
179views Bioinformatics» more  BIBE 2004»
15 years 7 months ago
Incorporating Ontology-Driven Similarity Knowledge into Functional Genomics: An Exploratory Study
This research explores the feasibility of semantic similarity approaches to supporting predictive tasks in functional genomics. It aims to establish potential relationships betwee...
Francisco Azuaje, Olivier Bodenreider
BIBE
2010
IEEE
137views Bioinformatics» more  BIBE 2010»
15 years 4 months ago
Comparison of Gene Prediction Programs for Metagenomic Data
This manuscript presents the most rigorous benchmarking of gene annotation algorithms for metagenomic datasets to date. We compare three different programs: GeneMark, MetaGeneAnnot...
Non Yok, Gail Rosen