数据库

Molecular genetic markers represent one of the most powerful tools for the analysis of genomes and the association of heritable traits with underlying genetic variation. The development of high-throughput methods for the detection of single nucleotide polymorphisms (SNPs) and si ...

Eukaryotic genomes are full of repetitive DNA, transposable elements (TEs) in particular, and accordingly there are a number of computational methods that can be used to identify TEs from genomic sequences. We present here a survey of two of the most readily available and widely used bioinform ...

Similarity searches are an essential component of most bioinformatic applications. They form the bases of structural motif identification, gene identification, and insights into functional associations. With the rapid increase in the available genetic data through a wide vari ...

The analysis of DNA sequence polymorphisms and SNPs (single nucleotide polymorphisms) can provide insights into the evolutionary forces acting on populations and species. Available population-genetic methods, and particularly those based on the coalescent theory, have bec ...

OrthologID (http://nypg.bio.nyu.edu/orthologid/) allows for the rapid and accurate identification of gene orthology within a character-based phylogenetic framework. The Web application has two functions – an orthologous group search and a query orthology classification. T ...

Compositional heterogeneity is a poorly appreciated attribute of aligned nucleotide and amino acid sequences. It is a common property of molecular phylogenetic data, and it has been found to occur across sequences and/or across sites. Most molecular phylogenetic methods assume that t ...

Multiple alignment of DNA sequences is an important step in various molecular biological analyses. As a large amount of sequence data is becoming available through genome and other large-scale sequencing projects, scalability, as well as accuracy, is currently required for a multiple s ...

Our understanding of the origins, the functions and/or the structures of biological sequences strongly depends on our ability to decipher the mechanisms of molecular evolution. These complex processes can be described through the comparison of homologous sequences in a phylogene ...

jModelTest is a bioinformatic tool for choosing among different models of nucleotide substitution. The program implements five different model selection strategies, including hierarchical and dynamical likelihood ratio tests (hLRT and dLRT), Akaike and Bayesian informat ...

Supertree methods combine multiple phylogenetic trees to produce the overall best “supertree.” They can be used to combine phylogenetic information from datasets only partially overlapping and from disparate sources (like molecular and morphological data), or to break down prob ...

Recombination between nucleotide sequences is a major process influencing the evolution of most species on Earth. While its evolutionary value is a matter of quite intense debate, so too is the influence of recombination on evolutionary analysis methods that assume nucleotide sequen ...

Natural selection is a fundamental process affecting all evolving populations. In the simplest case, positive selection increases the frequency of alleles that confer a fitness advantage relative to the rest of the population, or increases its genetic diversity, and negative select ...

Genome sequencing efforts have reformed the nature of biological inquiry, prompting the development of technologies for the functional annotation of mammalian genes. Based on methodologies originally discovered in plants and Caenorhabditis elegans, RNA interference has o ...

High-throughput methodologies have created new opportunities for studying biological phenomena in an unbiased manner. Using automated cell manipulations and microscopy platforms, it is now possible to easily screen entire genomes for genes that affect any cellular process th ...

Cellular processes are carried out through a series of molecular interactions. Various experimental approaches can be used to investigate these functional relationships on a large-scale. Recently, the power of investigating biological systems from the perspective of genetic ( ...

Peptide recognition modules (PRMs) play critical roles in cellular processes, including differentiation, proliferation and cytoskeleton organization. PRMs normally bind to short linear motifs in protein ligands, and by so doing recruit proteins into signaling complexes. Ba ...

Multiprotein complexes are essential building blocks for many cellular processes in an organism. Taking the process of transcription as an example, the interplay of several chromatin-remodeling complexes is responsible for the tight regulation of gene expression. Knowing how th ...

Proteome-wide analysis of protein C-termini has long been inaccessible, but is now enabled by a newly developed negative selection strategy we term C-terminomics. In this procedure, amine- and carboxyl groups of full-length proteins are chemically protected. After trypsin digesti ...

Secretagogin is a calcium-binding protein whose expression is characterised in neuroendocrine, pancreatic, and retinal cells. We have used an array-based proteomic approach with the prokaryotically expressed human protein array (hEx1) and the eukaryotically expressed hum ...

Protein complexes and protein–protein interactions (PPIs) are fundamental for most biological functions. Deciphering the extensive protein interaction networks that occur within cellular contexts has become a logical extension to the human genome project. Proteome-sca ...