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TCBB
2008
107views more  TCBB 2008»
9 years 10 months ago
Progressive Tree Neighborhood Applied to the Maximum Parsimony Problem
Abstract-- The Maximum Parsimony problem aims at reconstructing a phylogenetic tree from DNA sequences while minimizing the number of genetic transformations. To solve this NP-comp...
Adrien Goëffon, Jean-Michel Richer, Jin-Kao H...
NAR
2006
84views more  NAR 2006»
9 years 10 months ago
Zinc Finger Tools: custom DNA-binding domains for transcription factors and nucleases
Individual zinc finger (ZF) domains that recognize DNA triplets with high specificity and affinity can be used to create designer transcription factors and nucleases that are spec...
Jeffrey G. Mandell, Carlos F. Barbas III
BMCBI
2007
147views more  BMCBI 2007»
9 years 10 months ago
Comparative analysis of long DNA sequences by per element information content using different contexts
Background: Features of a DNA sequence can be found by compressing the sequence under a suitable model; good compression implies low information content. Good DNA compression mode...
Trevor I. Dix, David R. Powell, Lloyd Allison, Jul...
BMCBI
2007
152views more  BMCBI 2007»
9 years 10 months ago
Recodon: Coalescent simulation of coding DNA sequences with recombination, migration and demography
Background: Coalescent simulations have proven very useful in many population genetics studies. In order to arrive to meaningful conclusions, it is important that these simulation...
Miguel Arenas, David Posada
BMCBI
2006
121views more  BMCBI 2006»
9 years 10 months ago
Splice site identification using probabilistic parameters and SVM classification
Background: Recent advances and automation in DNA sequencing technology has created a vast amount of DNA sequence data. This increasing growth of sequence data demands better and ...
A. K. M. A. Baten, Bill C. H. Chang, Saman K. Halg...
BMCBI
2008
132views more  BMCBI 2008»
9 years 10 months ago
The SeqWord Genome Browser: an online tool for the identification and visualization of atypical regions of bacterial genomes thr
Background: Data mining in large DNA sequences is a major challenge in microbial genomics and bioinformatics. Oligonucleotide usage (OU) patterns provide a wealth of information f...
Hamilton Ganesan, Anna S. Rakitianskaia, Colin F. ...
BMCBI
2008
108views more  BMCBI 2008»
9 years 10 months ago
An analysis of the positional distribution of DNA motifs in promoter regions and its biological relevance
Background: Motif finding algorithms have developed in their ability to use computationally efficient methods to detect patterns in biological sequences. However the posterior cla...
Ana C. Casimiro, Susana Vinga, Ana T. Freitas, Arl...
BMCBI
2008
111views more  BMCBI 2008»
9 years 10 months ago
GENOMEPOP: A program to simulate genomes in populations
Background: There are several situations in population biology research where simulating DNA sequences is useful. Simulation of biological populations under different evolutionary...
Antonio Carvajal-Rodríguez
BMCBI
2008
132views more  BMCBI 2008»
9 years 10 months ago
The Average Mutual Information Profile as a Genomic Signature
Background: Occult organizational structures in DNA sequences may hold the key to understanding functional and evolutionary aspects of the DNA molecule. Such structures can also p...
Mark Bauer, Sheldon M. Schuster, Khalid Sayood
BMCBI
2010
108views more  BMCBI 2010»
9 years 10 months ago
An intuitionistic approach to scoring DNA sequences against transcription factor binding site motifs
Background: Transcription factors (TFs) control transcription by binding to specific regions of DNA called transcription factor binding sites (TFBSs). The identification of TFBSs ...
Fernando Garcia-Alcalde, Armando Blanco, Adrian J....
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