Impact of phylogeny on structural contact inference from protein sequence data
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Sequence motifs are of greater biological importance in nucleotide and protein sequences. The conserved occurrence of identical motifs represents the functional significance and helps to classify the biological sequences. In this paper, a new algorithm is ...
Phylogenetic bootstrapping (BS) is a standard technique for inferring confidence values on phylogenetic trees that is based on reconstructing many trees from minor variations of the input data, trees called replicates. BS is used with all phylogenetic reco ...
A fundamental requirement of quantitative palaeoecology is consistent taxonomy between a modern training set and palaeoecological data. In this study we assess the possible consequences of violation of this requirement by simulating taxonomic errors in tes ...
This article concerns the following question arising in computational evolutionary biology. For a given subclass of phylogenetic networks, what is the maximum value of 0
Recent comparative genomic and other large-scale bioinformatics studies increasingly have been using gene annotations, functional classifications, and complimentary data from the emerging “-omics” disciplines. Indeed, such analyses have better chances to u ...
The study of genorne rearrangement is much harder than the corresponding problems on DNA and protein sequences, because of the occurrences of numerous combinatorial structures. By explicitly exploring these combinatorial structures, the recently developed ...
The rapid accumulation of whole-genome data has renewed interest in the study of genomic rearrangements. Comparative genomics, evolutionary biology, and cancer research all require models and algorithms to elucidate the mechanisms, history, and consequence ...
PCBs are persistent organic pollutants which have entered the environment through both use and disposal. The environmental dissemination of PCBs is complex and nearly global in scale, although their production was banned in the 80’s. Nowadays, specific bac ...
Background: Reassortments are events in the evolution of the genome of influenza (flu), whereby segments of the genome are exchanged between different strains. As reassortments have been implicated in major human pandemics of the last century, their identi ...
Background: Reassortments are events in the evolution of the genome of influenza (flu), whereby segments of the genome are exchanged between different strains. As reassortments have been implicated in major human pandemics of the last century, their identi ...