Titlebook: Comparative Genomics; RECOMB 2006 Internat Guillaume Bourque,Nadia El-Mabrouk Conference proceedings 2006 Springer-Verlag Berlin Heidelberg

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A PQ Framework for Reconstructions of Common Ancestors and Phylogeny,versions and transpositions within the members of the species have also been made over the years. The task of constructing a phylogeny tree of the members of the same species, given this knowledge and data, is an important problem. In this context, a key observation is that the “distance” between tw

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Intron Loss Dynamics in Mammals, mammalian genes. We found no evidence for intron gain and 122 cases of intron loss, most of which occurred within the rodent lineage. Majority (68%) of the deleted introns were extremely small (<150 bp), significantly smaller than average. The intron losses occurred almost exclusively within highly

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Finding Maximum Likelihood Indel Scenarios,most likely scenario of insertions and deletions capable of explaining the gaps observed in the alignment. This problem, that we called the Indel Maximum Likelihood Problem (IMLP), is an important step toward the reconstruction of ancestral genomics sequences, and is important for studying evolution

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Conservation Patterns in ,-Elements Reveal Compensatory Mutations,nts. A better understanding and modelling of the TF-DNA interaction is an important area of research. The Positional Weight Matrix (PWM) is the most common model of TF-DNA binding and it presumes that the nucleotide preferences at individual positions within the binding site are independent. However

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Transcription Factor Centric Discovery of Regulatory Elements in Mammalian Genomes Using Alignment-y been partially addressed in prokaryotes and lower eukaryotes. Given the higher length of regulatory regions and the relative low complexity of DNA binding signature, however, methods to address this problem in higher order eukaryotes are lacking. In this paper, we propose a novel computational fra

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Identifiability Issues in Phylogeny-Based Detection of Horizontal Gene Transfer,ificance on understanding prokaryotic genome diversification and unraveling their complexities. Phylogeny-based detection of HGT is one of the most commonly used approaches for this task, and is based on the fundamental fact that HGT may cause gene trees to disagree with one another, as well as with

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Software Engineering and Environmentw that dependent positions are more likely to be functional, as evidenced by a higher information content and higher conservation. We discuss two examples—Elk-1 and SAP-1 where the inferred compensatory mutation is consistent with known TF-DNA crystal structure.

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