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SOFTWARE ARTICLE Open Access WordCluster: detecting clusters of DNA words and genomic elements
"... Background: Many k-mers (or DNA words) and genomic elements are known to be spatially clustered in the genome. Well established examples are the genes, TFBSs, CpG dinucleotides, microRNA genes and ultra-conserved non-coding regions. Currently, no algorithm exists to find these clusters in a statisti ..."
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statistically comprehensible way. The detection of clustering often relies on densities and sliding-window approaches or arbitrarily chosen distance thresholds. Results: We introduce here an algorithm to detect clusters of DNA words (k-mers), or any other genomic element, based on the distance between
Nonrandom clusters of palindromes in Herpesvirus genomes.
- J. Computational Biology
, 2005
"... ABSTRACT Palindromes are symmetrical words of DNA in the sense that they read exactly the same as their reverse complementary sequences. Representing the occurrences of palindromes in a DNA molecule as points on the unit interval, the scan statistics can be used to identify regions of unusually hig ..."
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Cited by 16 (9 self)
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ABSTRACT Palindromes are symmetrical words of DNA in the sense that they read exactly the same as their reverse complementary sequences. Representing the occurrences of palindromes in a DNA molecule as points on the unit interval, the scan statistics can be used to identify regions of unusually
DNA Genome-based Diagnostics for Athletes ’ Physiological Conditions Using Cluster Analysis
, 2008
"... Abstract. A system of cluster analyses for gene expression signatures from cDNA microarrays is described to diagnose athletes ’ physiological conditions in response to training loads, which uses standard statistical algorithms to arrange altered genes according to similarity in the patterns of gene ..."
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seen in gene expression signatures indicates the status of cellular processes, our results suggest a strategy to “see ” training-induced cellular processes based on all of the 39 altered genes with cDNA microarrays. Key words: cluster analysis, physiological conditions, gene expression signatures, cDNA
An Effective Method for Detecting Gene Conversion Events in Whole Genomes
"... Gene conversion events are often overlooked in analyses of genome evolution. In a conversion event, an interval of DNA sequence (not necessarily containing a gene) overwrites a highly similar sequence. The event creates relationships among genomic intervals that can confound attempts to identify ort ..."
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Cited by 2 (0 self)
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Gene conversion events are often overlooked in analyses of genome evolution. In a conversion event, an interval of DNA sequence (not necessarily containing a gene) overwrites a highly similar sequence. The event creates relationships among genomic intervals that can confound attempts to identify
Word count:
, 2009
"... The computational approach to the study of transcription regulation has become more attractive. It is sufficiently mature to influence the design of the laboratory procedure to detect the transcription factor that regulates the gene and the corresponding transcription factor binding sites. With the ..."
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. With the accumulation of genome sequences, combined with effective gene-prediction algorithms, comparing genomic sequences across species – phylogenetic footprinting – rapidly become a very effective approach to identify functionally important DNA sequences. Programs such as BigFoot are created based on this principle
Automatic Detection of Gene Clusters by P-Quasi Complete Linkage Grouping
"... Introduction It is known that bacteria genomes are highly organized to express functions cooperatively, for instance, by operons or by locating related genes adjacently on the genome for the transcriptional advantage. Since the complete sequences of several genomes were released, the gene clusters ..."
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Cited by 1 (0 self)
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Introduction It is known that bacteria genomes are highly organized to express functions cooperatively, for instance, by operons or by locating related genes adjacently on the genome for the transcriptional advantage. Since the complete sequences of several genomes were released, the gene clusters
MM: Clustering of genes coding for DNA binding proteins in a region of atypical evolution of the human genome
- J Mol Evol
"... Abstract. Comparison of the human and mouse genomes has revealed that significant variations in evolutionary rates exist among genomic regions and that a large part of this variation is interchromo-somal. We confirm in this work, using a large col-lection of introns, that human chromosome 19 is the ..."
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Cited by 6 (2 self)
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and mouse genomes. It is likely that the overall high synonymous and intron rates in chromosome 19 are a by-product of the high GC content of this chromo-some. Key words: Chromosome 19 — DNA binding
Identification of Genomic Markers by RAPD-PCR Primer in Leukemia Patients
"... Abstract: The aim of this study is to ascertain the possible application of Random Amplification of Polymorphic DNA (RAPD) analysis as a genetic test to investigate DNA polymorphisms and detection of genomic markers in various types of leukemia. The results showed unique profiles of amplified DNA fr ..."
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Abstract: The aim of this study is to ascertain the possible application of Random Amplification of Polymorphic DNA (RAPD) analysis as a genetic test to investigate DNA polymorphisms and detection of genomic markers in various types of leukemia. The results showed unique profiles of amplified DNA
Genome-Wide Evolutionary Characterization and Expression Analyses of WRKY Family Genes in Brachypodium distachyon. DNA Res: dst060
, 2014
"... Membersof plantWRKY gene family are ancient transcription factors that function inplant growthandde-velopment and respond tobiotic and abiotic stresses. In our present study,wehave investigatedWRKY family genes in Brachypodium distachyon, a new model plant of family Poaceae. We identified a total of ..."
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Cited by 1 (0 self)
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of 86WRKY genes from B. distachyon and explored their chromosomal distribution and evolution, domain alignment, promoter cis-elements, and expression profiles. Combining the analysis of phylogenetic tree of BdWRKY genes and the result of expressionprofiling, results showed thatmost of clustered
Statistical Learning for Detecting Protein-DNA-Binding Sites
"... Abstract — Detecting the sites on genomic DNA at which DNA binding proteins bind is a highly relevant task in bioinformatics. For example, the bindings sites of transcription factors are key elements of regulatory networks and determine the location of genes on a genome. Usually, for a given DNA bin ..."
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Abstract — Detecting the sites on genomic DNA at which DNA binding proteins bind is a highly relevant task in bioinformatics. For example, the bindings sites of transcription factors are key elements of regulatory networks and determine the location of genes on a genome. Usually, for a given DNA
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