XML Presentation of Documents Used for Data Exchange in Management of Genetic Resources

In the global strategy for preservation genetic resources of farm animals the implementation of information technology is of great importance. In this regards platform independent information tools and approaches for data exchange are needed in order to obtain aggregate values for regions and countries of spreading a separate breed. The current paper presents a XML based solution for data exchange in management genetic resources of farm animals’ small populations. There are specific requirements to the exchanged documents that come from the goal of data analysis. Three main types of documents are distinguished and their XML formats are discussed. DTD and XML Schema for each type are suggested. Some examples of XML documents are given also.

Derivation of Context-free Stochastic L-Grammar Rules for Promoter Sequence Modeling Using Support Vector Machine

Formal grammars can used for describing complex repeatable structures such as DNA sequences. In this paper, we describe the structural composition of DNA sequences using a context-free stochastic L-grammar. L-grammars are a special class of parallel grammars that can model the growth of living organisms, e.g. plant development, and model the morphology of a variety of organisms. We believe that parallel grammars also can be used for modeling genetic mechanisms and sequences such as promoters. Promoters are short regulatory DNA sequences located upstream of a gene. Detection of promoters in DNA sequences is important for successful gene prediction. Promoters can be recognized by certain patterns that are conserved within a species, but there are many exceptions which makes the promoter recognition a complex problem. We replace the problem of promoter recognition by induction of context-free stochastic L-grammar rules, which are later used for the structural analysis of promoter sequences. L-grammar rules are derived automatically from the drosophila and vertebrate promoter datasets using a genetic programming technique and their fitness is evaluated using a Support Vector Machine (SVM) classifier. The artificial promoter sequences generated using the derived L- grammar rules are analyzed and compared with natural promoter sequences.