COMPRESSION BASED CLASSIFICATION OF PRIMATE ENDOGENOUS RETROVIRUS SEQUENCES (2009)
Vladimir Kuryshev, Pavol Hanus
The highly divergent character of retrovirus sequences makes cross family alignment based classification of whole genomes difficult and unreliable. Standard methods thus focus on alignment based...
Information Theoretic Distance Measures in (2009)
Pavol Hanus, Janis Dingel, Juergen Zech, Joachim Hagenauer, Jakob C. Mueller
Abstract — A variety of distance measures has been developed in information theory, proven useful in the application to digital information systems. According to the fact, that the information for...
1 An Alternative Method for Detecting Conserved Elements in Multiple Sequence Alignments (2009)
Pavol Hanus, Janis Dingel, Joachim Hagenauer, Jakob C. Mueller
Abstract — We present an alternative method for detecting conserved regions in multiple sequence alignments. In contrast to earlier approaches, we avoid using assumptions about neutral substitution...
Molecular Genetics · Classification (2009)
Pavol Hanus, Bernhard Goebel, Janis Dingel, Johanna Weindl, Juergen Zech, Zaher Dawy, ...
Abstract The DNA sequencing efforts of the past years together with rapid progress in sequencing technology have generated a huge amount of sequence data available in public molecular databases. This...
Local conservation scores without a priori assumptions on neutral substitution rates (2008)
Dingel, Janis, Hanus, Pavol, Leonardi, Niccolò, Hagenauer, Joachim, Zech, Jürgen, Mueller, Jakob C
Abstract Background Comparative genomics aims to detect signals of evolutionary conservation as an indicator of functional constraint. Surprisingly, results of the ENCODE project revealed that about...
Zaher Dawy, Joachim Hagenauer, Pavol Hanus, Jakob C. Mueller
Abstract — Possibilities of using mutual information for classification and content recognition are exploited. Two different mutual information based distance measures are proposed, one for...
Weindl, Johanna, Hanus, Pavol, Dawy, Zaher, Zech, Juergen, Hagenauer, Joachim, Mueller, Jakob C.
We present a computational model of DNA-binding by σ70 in Escherichia coli which allows us to extract the functional characteristics of the wider promoter environment. Our model is based on a...