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It involves several distinct steps, as outlined in the image below. Changing any one of the steps will change the outcome of the analysis, so the MAQC Project [2] was created to identify a set of standard strategies. Companies exist that use the MAQC protocols to perform a complete analysis. [3] The steps required in a microarray experiment
Structural bioinformatics is the branch of bioinformatics that is related to the analysis and prediction of the three-dimensional structure of biological macromolecules such as proteins, RNA, and DNA. It deals with generalizations about macromolecular 3D structures such as comparisons of overall folds and local motifs, principles of molecular ...
Most published studies using ChIP-on-chip repeat their experiments at least three times to ensure biologically meaningful maps. The cost of the DNA microarrays is often a limiting factor to whether a laboratory should proceed with a ChIP-on-chip experiment. Another limitation is the size of DNA fragments that can be achieved.
Analysis Utility Branch Dose–response curves: Graph that shows the magnitude of the response of an organism, as a function of exposure (or doses) to a stimulus or stressor (usually a chemical) after a certain exposure time [2]
Databases are essential for bioinformatics research and applications. Databases exist for many different information types, including DNA and protein sequences, molecular structures, phenotypes and biodiversity. Databases can contain both empirical data (obtained directly from experiments) and predicted data (obtained from analysis of existing ...
Experiment and statistical analysis: This is when the experiment is really implemented following the appropriate experimental design, data is collected and the more suitable statistical tests are evaluated. Inference: Is made when the null hypothesis is rejected or not rejected, based on the evidence that the comparison of p-values and α brings.
Biological data has also been difficult to define, as bioinformatics is a wide-encompassing field. Further, the question of what constitutes as being a living organism has been contentious, as "alive" represents a nebulous term that encompasses molecular evolution, biological modeling, biophysics, and systems biology.
Data analysis usually requires a combination of bioinformatics software tools (see also List of RNA-Seq bioinformatics tools) that vary according to the experimental design and goals. The process can be broken down into four stages: quality control, alignment, quantification, and differential expression. [ 105 ]