Bioinformatics defined

However, there are a number of issues here. In the first place, stress itself is a somewhat nebulous concept, and there is continuing debate about how it should be defined. Second, even with the benefit of multivariate statistics and the techniques of bioinformatics, measuring stress from all sources in a meaningful way is dauntingly complex and may not be realizable in practice. 

In this respect, the CUE domain is not a isolated case. There are a number of other domain families, each of them only defined in the bioinformatical sense, that have significant matches within established UBA or CUE domain regions. Based on this similarity and on secondary-structure predictions, it can be expected that all of those domain types assume the typical UBA-like three-helix bundle fold. However, it is not clear if all of those domains also bind to ubiquitin, or if they have evolved to different binding properties. Many of the UBA-like domain classes are unpublished. Nevertheless, they should be briefly discussed here, as they are a logical extension of the UBA/CUE paradigm. 

Ihmels, ]., Bergmann, S., and Brkai, N. (2004) Defining transcription modules using large-scale gene expression data. Bioinformatics 20, 1993-2003. 

If PMF and sequence homology searches fail using available protein and EST databases, mass spectrum data can, in principle, be used to search genome databases (GenBank http //www.ncbi.nlm.nih.gov/). However, only a small percentage of large genomic sequences code for proteins such that bioinformatics still needs to accurately define exon-intron structures (Andersen and Mann, 2000). 

FIGURE 1 Example of a gel-free-oriented proteomics nano-LC/MS-MS workflow in which bacterial culture proteins digested to tryptic peptides are separated via LC and peptides subsequently analyzed by mass spectrometry. In the process, the spectrometer rapidly cycles every few seconds and examines a size window in which peptide-derived MSI ions are analyzed to define MS/MS (MS2) spectra. The MS/MS (MS2) spectrum generated for each peptide then enters a bioinformatic pipeline for sequence identification, statistical validation, and quantification. 

The MIAME standard defines the minimum information investigators must report for a microarray experiment to be reproduced. The MAGE standard was born partially from MIAME, and the European Bioinformatics Institute used MIAME and MAGE to guide the development of ArrayEx-press, their public genomic data repository (34). Sample annotation lies at the heart of MIAME, underscoring the need to understand as completely as possible the experimental conditions that may influence the microarray data. Many journals that publish microarray data require the submission of MIAME-supportive microarray data to a public genomic data repository as a condition of publication. These typically include submission of protocols species, strains, and sex used for in vivo studies cell line name and culture conditions for in vitro studies, and other relevant information. 

As science has become increasingly specialized over the past two decades, so too has the area of bioinformatics. There are numerous specialized databases that deal with different aspects of biology. Some of these specialize in the area of proteins, while others specialize in the area of DNA. In general, these sites differ in two respects the general database(s) from which they draw information, and the parameters that they require the user to define to conduct the search. For instance, the AA Analysis database searches the more general SwissProt database to identify or group proteins on the basis... 

The field of bioinformatics has been defined in many ways and encompasses a large variety of areas of study. Within this scope, the common bond is genomic data, including its maintenance, analysis, and integration. In this chapter we retain this focus, providing an overview of various concepts of interest to researchers in the field of Toxicology. 

Unfortunately the vocabulary of biology is often imprecise. The terms computational biology and bioinformatics are interchangeable in some circles. Here we define computational biology as specifically focusing on the use of... 

Bioinformatics is a new and exciting subject developing its own methodologies, approaches and nomenclature with an elan which has not suffered from lack of precision about defining exactly what the subject is. As might be expected of a product of the computer age, it depends heavily on internet and database access, which are the essential tools of what has become termed in silico research. A very readable introduction to the subject is provided by Attwood and Parry-Smith (1999). 

A third virus that is structurally similar to BTV is rice dwarf virus (RDV) for which a cryo-EM reconstruction at a nominal resolution of 6.8 A has been obtained (Zhou et al., 2001). Bioinformatics coupled with novel methods in electron density map analysis were used to define the organization of secondary structure elements within the density and identify the primary sequences that form them (Zhou et al., 2001). This involved identifying tubular density corresponding to helices in assigning structure de novo and comparing regions of the viral structural proteins with domains of known folds (Zhou et al, 2001). The organization of RDV revealed was similar to that of BTV. 

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