基因表达差异显示实验

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 ...

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, ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

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 ...

Synthetic peptides are widely used for production and analysis of antibodies as well as in the study of protein modification enzymes. To circumvent the technical challenges of the existing techniques regarding peptide quantization and normalization, a new method of producing pepti ...

Protein microarray is a powerful tool for identifying disease biomarkers and therapeutical targets, and for systematically studying biological pathways with high efficiency. Although the protein microarray platform has been adopted by proteomic research and discovery, wh ...

Here, we provide methods for the creation of protein microarrays in microplates. The microplate consists of 96 wells with each well capable of holding a protein microarray at a spot density of up to 400 (20 � 20) individual elements. Arrays of capture monoclonal antibodies, corresponding to spec ...

Microarray technology has its roots in high-throughput parallel synthesis of biomacromolecules, combined with combinatorial science. In principle, the preparation of arrays can be performed either by in situ synthesis of biomacromolecules on solid substrates or by spotting of ex ...

As more genomes are sequenced, challenge of rapidly unraveling the functions of genes was faced. To that end, cell microarrays have been recently described that permit transfection of thousands of nucleic acids in parallel and enable the analysis of phenotypic consequences of such pertu ...

A protocol for quantification of oligonucleotide hybridization on polymer microparticles by europium(III) ion fluorescence is described. The procedure involves modification of commercially available amino-functionalized microparticles in such a manner that oligo ...