Context analysis

There is not usually a clear order in which to perform context analysis ("use-case analysis") and system behavioral specification. There is some element of negotiation between... 

V. V. Solov ev and I. B. Rogozin, Context Packet of Programs for Context Analysis of Sequences of DNA, RNA, and Proteins, 1 Search for the Homology and Functional Sites, Inst. Tsitologii i Genetiki, Novosibirsk, USSR, 1986. 

STRING string.embl.de No restriction PPIs derived from genomic context analysis, experiments, coexpression and literature-based (cover 179 species) von Mering et al. (2005)... 

Tabk 2 lists the number ofWD-repeat protein sequences identified with high confidence within various taxonomic divisions for particular species representatives. The numbers were obtained using simple sequence pattern recognition tools followed by a fiill-length protein sequence context analysis. They are presented in terms of the number of probable WD repeats and whether or not they contain additional domains of significant length. 

Carbohydrate hydroxyl groups are alkylated in three contexts analysis of polysaccharide sequences, dealt with in Section 4.2.1 protection of OH groups during synthetic transformations, which requires the alkyl residues to be removable and the modification of cheap polysaccharides, such as starch and cellulose, for more desirable properties. 

Doerks, T., von Mering, C., and Bork, P. (2004) Functional clues for hypothetical proteins based on genomic context analysis in prokaryotes. Nucl. Acids Res. 32, 6321-6326. 

Fig. 1. Main window of the software package ANACONDA for two-codon context analysis at the ORFeome map level. The left panel presents a hierarchical tree of all genomes under analysis by ANACONDA. The Tab Valid includes all individual ORFs used to determine context bias and to build the respective map, whereas the Tab Reject allows visual inspection of ORFs that do not comply with the criteria selected during the opening of the ORFeome. An ORFeomic map for two-codon context bias obtained with the total set of predicted coding sequences of Thermotoga maritima (accession number AE000512 from GenBank), is shown.

Fig. 2. Main window of the software package ANACONDA for two-codon context analysis in total genomes at the gene view level. Individual ORFs that were used to calculate codon context bias are shown in the hierarchical left panel. Clicking on one of them changes the main panel into the gene view layout. This is composed of a header with the name of the ORF as stated in the original file and the sequence itself. This sequence is colored according to the residual color scale obtained for that ORFeome, i.e., each codon pair is colored in the ORF sequence with the same color scale that it had in the ORFeome map for two-codon contexts. Rare codons are highlighted using circles.

Fig. 3. Main window of the software package ANACONDA for two-codon context analysis at the ORFeome comparison level. When more than three ORFeomes are processed by ANACONDA it is possible to build a large-scale comparative map, as shown in the main right panel of the software s window. In this map, each column represents one ORFeome, with one line for all possible combinations of two consecutive codons. Visual comparison of different ORFeomes is possible if all ORFeomes are normalized to a given size and aligned using the same context order.

Moura, G., Pinheiro, M., Silva, R., et al. (2005) Comparative context analysis of codon pairs on an ORFeome scale. Genome Biol. 6, R28. 

Ciria, R., C. Abreu-Goodger, E. Morett, and E. Merino. 2004. GeConT Gene context analysis. Bioinformatics 20 2307-8. 

Buck, P. (1984). Kontextanalyse des energiebegriffes. [Context analysis of the energy concept], Dirfflcft cfl, 11, 176-196. 

Correlation and contingeiKy (symptom-context) analysis across systemic levels, as suggested in triple-response models (multimodal assessment) ... 

Expression Context Analysis This phase analyzes each expression in the behavior and determines how it is used in relation to the expressions surrounding it. For instance, the result of an expression may be used only as a memory address. This information is recorded and used later by a synthesis phase to assign an appropriate type of register to the expression. As for Execution Unit Organization Analysis, this phase is specific to microprocessor design. 

The contexts were determined by the context analysis phase before code generation. 

Vieira, M.F.Q. Ademar, V.S. Aguiar, Y.C. Scherer, D. Context Analysis During Task Execution An Operator Model. In lADIS International Conference Interfaces and Human Computer Interaction, Algarve, Portugal. Proceedings of lADIS. pp. 113-120.2009. 

The result of the context analysis is an input-output model with assumptions about environmental effects that can be ignored. In the case of the thermometer it is assumed that only the medium temperature is relevant and that the heat transfer conditions are constant. 

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