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JCB
2006
124views more  JCB 2006»
13 years 7 months ago
The Average Common Substring Approach to Phylogenomic Reconstruction
We describe a novel method for efficient reconstruction of phylogenetic trees, based on sequences of whole genomes or proteomes, whose lengths may greatly vary. The core of our me...
Igor Ulitsky, David Burstein, Tamir Tuller, Benny ...
BMCBI
2005
130views more  BMCBI 2005»
13 years 7 months ago
Squid - a simple bioinformatics grid
Background: BLAST is a widely used genetic research tool for analysis of similarity between nucleotide and protein sequences. This paper presents a software application entitled &...
Paulo C. Carvalho, Rafael V. Glória, Antoni...
BMCBI
2005
127views more  BMCBI 2005»
13 years 7 months ago
Genomes are covered with ubiquitous 11 bp periodic patterns, the "class A flexible patterns"
Background: The genomes of prokaryotes and lower eukaryotes display a very strong 11 bp periodic bias in the distribution of their nucleotides. This bias is present throughout a g...
Etienne Larsabal, Antoine Danchin
BMCBI
2004
166views more  BMCBI 2004»
13 years 7 months ago
Gene prediction using the Self-Organizing Map: automatic generation of multiple gene models
Background: Many current gene prediction methods use only one model to represent proteincoding regions in a genome, and so are less likely to predict the location of genes that ha...
Shaun Mahony, James O. McInerney, Terry J. Smith, ...
BMCBI
2011
13 years 2 months ago
Shape-based peak identification for ChIP-Seq
Background: The identification of binding targets for proteins using ChIP-Seq has gained popularity as an alternative to ChIP-chip. Sequencing can, in principle, eliminate artifac...
Valerie Hower, Steven N. Evans, Lior Pachter