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PhyME: A Software tool for Finding Motifs in Sets of Orthologous Sequences

Discovery of transcription factor binding sites is a crucial and challenging problem in bioinformatics. Several computational tools have been developed for this problem, popularly known as the motif-finding problem. PhyME is an ab initio motif-finding algorithm, which finds over ...

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Comparative Genomics-Based Orthologous Promoter Analysis Using the DoOP Database and the DoOPSearch Web Tool

Bioinformatic and experimental analyses of promoter regions are available for a long time. Finding of the transcription factor binding sites (TFBSs), however, by either method still faces a number of problems. For example, because of the ambiguity of binding of transcription factors, the ...

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Fastcompare: A Nonalignment Approach for Genome-Scale Discovery of DNA and mRNA Regulatory Elements Using Network-Level Conservation

Here, we describe the usage of Fastcompare, a simple and efficient comparative approach for finding short noncoding DNA (e.g., transcription factor binding sites) and mRNA (e.g., microRNA target sites) sequences that are globally conserved between two genomes. Fastcompare is based on the ...

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Discovery of Motifs in Promoters of Coregulated Genes

We present a method to predict cis-acting elements by detecting over-represented motifs in promoters of a set of coregulated genes (single-genome, multigenes approach). The method has been used successfully to detect regulating elements in bacteria and yeast. It can be used with higher or ...

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Phylogenetic Footprinting to Find Functional DNA Elements

Phylogenetic footprinting is powerful technique for finding functional elements from sequence data. Functional elements are thought to have greater sequence constraint than nonfunctional elements, and, thus, undergo a slower rate of sequence change through time. Phylogene ...

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Using the Gibbs Motif Sampler for Phylogenetic Footprinting

The Gibbs Motif Sampler (Gibbs) is a software package used to predict conserved elements in biopolymer sequences. Although the software can be used to locate conserved motifs in protein sequences, its most common use is the prediction of transcription factor binding sites (TFBSs) in promot ...

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Detecting Regulatory Sites Using PhyloGibbs

PhyloGibbs is a program that uses Gibbs sampling to predict putative binding sites for transcription factors in DNA. It has two notable advances over previous algorithms for this task: it handles phylogenetically related sequence systematically, and it evaluates the significance of ...

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Web-Based Identification of Evolutionary Conserved DNA cis-Regulatory Elements

Transcription regulation on a gene-by-gene basis is achieved through transcription factors, the DNA-binding proteins that recognize short DNA sequences in the proximity of the genes. Unlike other DNA-binding proteins, each transcription factor recognizes a number of sequences, ...

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Exploring Conservation of Transcription Factor Binding Sites with CONREAL

Prediction of transcription factor binding sites (TFBS) is commonly used to formulate working hypotheses for experimental studies on gene regulation. Computational identification of functional TFBS is complicated because of short length and degeneracy of sequence motifs re ...

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Comparative Analysis of RNA Genes: The caRNAc Software

RNA genes are ubiquitous in the cell and are involved in a number of biochemical processes. Because there is a close relationship between function and structure, software tools that predict the secondary structure of noncoding RNAs from the base sequence are very helpful. In this article, we foc ...

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Computational and Statistical Methodologies for ORFeome Primary Structure Analysis

Codon usage and context are biased in open reading frames (ORFs) of most genomes. Codon usage is largely influenced by biased genome G+C pressure, in particular in prokaryotes, but the general rules that govern the evolution of codon context remain largely elusive. To shed new light into this quest ...

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Efficient Annotation of Bacterial Genomes for Small, Noncoding RNAs Using the Integrative Computational Tool sRNAPredict2

sRNAs are small noncoding RNAs that have been shown to perform diverse regulatory roles in a number of prokaryotes. Although several bioinformatic approaches have proven effective in identifying bacterial sRNAs, implementing these approaches presents significant computat ...

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Prediction of Structural Noncoding RNAs With RNAz

The function of many noncoding RNAs (ncRNAs) depend on a defined secondary structure. RNAz detects evolutionarily conserved and thermodynamically stable RNA secondary structures in multiple sequence alignments and, thus, efficiently filters for candidate ncRNAs. In this cha ...

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Methods for Multiple Alignment and Consensus Structure Prediction of RNAs Implemented in MARNA

Multiple alignments of RNAs are an essential prerequisite to further analyses such as homology modeling, motif description, or illustration of conserved or variable binding sites. Beyond the comparison of RNAs on the sequence level, structural conformations determined by basepa ...

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Design and Fabrication of Spotted Long Oligonucleotide Microarrays for Gene Expression Analysis

DNA microarray technology has advanced rapidly since the first use of cDNA microarrays almost a decade ago. For gene expression studies on organisms, for which the genomes have been sequenced, cDNA microarrays are being gradually replaced by gene-specific oligonucleotide microarr ...

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Construction of In Situ Oligonucleotide Arrays on Plastic

The concept of DNA arrays was first introduced in the early 1980s, by Sir Edwin Southern. Since then, many research institutions and biotechnology companies have investigated the potential use of arrays in fields ranging from genetic diagnostics to forensics investigations. A 64-chan ...

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Detecting Ligated Fragments on Oligonucleotide Microarrays: Optimizing Chip Design, Array Multiplex Ligation-Dependent Probe Amplification Modificatio

Copy-number polymorphisms at specific genomic loci have been implicated in numerous human and animal disease phenotypes. Multiplex ligation-dependent probe amplification (MLPA) is a molecular genetic technique allowing targeted quantification of genomic copy-number ...

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Detection of Single-Nucleotide Polymorphisms in Cancer-Related Genes by Minisequencing on a Microelectronic DNA Chip

The ability to realize simultaneous genotyping of multiple single-nucleotide polymorphisms or mutations is valuable in DNA samples from complex multigenic pathologies such as cancer. In this way, the complexity (number of hybridization units per chip) of the developed MICAM? DNA ch ...

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In Situ Synthesis of Peptide Microarrays Using Ink-Jet Microdispensing

The study of protein-protein and protein-DNA interactions is critical to understand biological processes. This article presents the methodology to create peptide microarrays in situ for the high-throughput screening of complex biomolecules. The in situ ink-jet peptide synthe ...

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Hybridization Analysis Using Oligonucleotide Probe Arrays

This chapter describes methodology for the labeling, hybridization, and detection of amplicon target DNA to arrays of oligonucleotide probes attached to plastic substrates. A systematic approach to target discrimination based on both hybridization and wash stringency is prov ...

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