Polynesian genetic affinities to populations of Asia were studied using mtDNA markers. A total of 1,037 individuals from 12 populations were screened for a 9-bp deletion in the intergenic region between the COil and tRNALYS genes that approaches fixation in Polynesians. Sequence-specific oligonucleotide probes that identify specific mtDNA control region nucleotide substitutions were used to des...

We propose a representation for gene expression data called conserved gene expression motifs or xmotifs. A gene’s expression level is conserved across a set of samples if the gene is expressed with the same abundance in all the samples. A conserved gene expression motif is a subset of genes that is simultaneously conserved across a subset of samples. We present a computational technique to disc...

We propose a representation for gene expression data called conserved gene expression motifs or XMOTIFs. A gene's expression level is conserved across a set of samples if the gene is expressed with the same abundance in all the samples. A conserved gene expression motif is a subset of genes that is simultaneously conserved across a subset of samples. We present a computational technique to disc...

Type I restriction enzymes bind to specific DNA sequences but subsequently translocate non-specific DNA past the complex in a reaction coupled to ATP hydrolysis and cleave DNA at any barrier that can halt the translocation process. The restriction subunit of these enzymes, HsdR, contains a cluster of seven amino acid sequence motifs typical of helicase superfamily II, that are believed to be re...

The information theory has been used for quite some time in the area of computational biology. In this paper we discuss and improve the function Entropic Profile, introduced by Vinga and Almeida in [23]. The Entropic Profiler is a function of the genomic location that captures the importance of that region with respect to the whole genome. We provide a linear time linear space algorithm called ...

1. introduction some narratologists like kristeva and genette believe that if a text remembers another text, a dialogue has taken place between them and an inter-textual (or trans-textual) relationship has thus been established. some also believe that there is always a relationship between texts. among them, genette accompanied his claims by a theory and opened a new way before the narratologis...

We present a method for inference of transcriptional modules from heterogeneous data sources. It allows identifying the responsible set of regulators in combination with their corresponding DNA recognition sites (motifs) and target genes. Our approach distinguishes itself from previous work in literature because it fully exploits the knowledge of three independently acquired data sources: ChIPc...

IP6 Kinases (IP6Ks) are important mammalian enzymes involved in inositol phosphates metabolism. Although IP6K has not yet been identified in plant chromosomes, there are many clues suggesting its presence in vegetal cells. In particular, there are observations suggesting that the corresponding gene might be found in plant mtDNA, encrypted and hidden by virtue of editing and/or trans splicing pr...

Protocol S1: A brief review of DNA motif finding Hilal Kazan1, Debashish Ray2, Esther T Chan3, Timothy R Hughes2,3,4, Quaid Morris1,2,3,4,∗ 1 Department of Computer Science, University of Toronto, Toronto, Ontario, Canada 2 Banting and Best Department of Medical Research, University of Toronto, Toronto, Ontario, Canada 3 Department of Molecular Genetics, University of Toronto, Toronto, Ontario,...

GenericBioMatch is a novel algorithm for exact match in biological sequences. It allows the sequence motif pattern to contain one or more wild card letters (eg. Y, R, W in DNA sequences) and one or more gaps of any number of bases. GenericBioMatch is a relatively fast algorithm as compared to probabilistic algorithms, and has very little computational overhead. It is able to perform exact match...