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» Parameters for accurate genome alignment
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ICCS
2005
Springer
14 years 1 months ago
SWAT: A New Spliced Alignment Tool Tailored for Handling More Sequencing Errors
Abstract. There are several computer programs that align mRNA with its genomic counterpart to determine exon boundaries. Though most of these programs perform such alignment effici...
Yifeng Li, Hesham H. Ali
BMCBI
2005
169views more  BMCBI 2005»
13 years 7 months ago
MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes
Background: Cis-regulatory modules are combinations of regulatory elements occurring in close proximity to each other that control the spatial and temporal expression of genes. Th...
Voichita D. Marinescu, Isaac S. Kohane, Alberto Ri...
BMCBI
2008
89views more  BMCBI 2008»
13 years 7 months ago
Increasing the efficiency of bacterial transcription simulations: When to exclude the genome without loss of accuracy
Background: Simulating the major molecular events inside an Escherichia coli cell can lead to a very large number of reactions that compose its overall behaviour. Not only should ...
Marco A. J. Iafolla, Guang Qiang Dong, David R. Mc...
BMCBI
2010
120views more  BMCBI 2010»
13 years 7 months ago
Estimating true evolutionary distances under rearrangements, duplications, and losses
Background: The rapidly increasing availability of whole-genome sequences has enabled the study of whole-genome evolution. Evolutionary mechanisms based on genome rearrangements h...
Yu Lin, Vaibhav Rajan, Krister M. Swenson, Bernard...
JCB
2007
107views more  JCB 2007»
13 years 7 months ago
Effects of Long-Range Correlations in DNA on Sequence Alignment Score Statistics
Long-range correlations in genomic base composition are a ubiquitous statistical feature among many eukaryotic genomes. In this article, these correlations are shown to substantia...
Philipp W. Messer, Ralf Bundschuh, Martin Vingron,...