The Pathway Tools Pathway Prediction Algorithm
نویسندگان
چکیده
منابع مشابه
The Pathway Tools Pathway Prediction Algorithm
The PathoLogic component of the Pathway Tools software performs prediction of metabolic pathways in sequenced and annotated genomes. This article provides a detailed presentation of the PathoLogic algorithm. The algorithm consists of two phases. The reactome inference phase infers the reactions catalyzed by the organism from the set of enzymes present in the annotated genome. The pathway infere...
متن کاملThe Pathway Tools software
MOTIVATION Bioinformatics requires reusable software tools for creating model-organism databases (MODs). RESULTS The Pathway Tools is a reusable, production-quality software environment for creating a type of MOD called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc (see http://ecocyc.org) integrates our evolving understanding of the genes, proteins, metabolic network, and genetic ne...
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Pathways are crucial to our understanding of biology. The speed at which new organisms are being sequenced is outstripping our ability to experimentally determine their biochemical pathway information. In recent years several initiatives have been successful in automating the annotations of individual proteins in these organisms, either experimentally or by prediction. However, to leverage the ...
متن کاملThe Pathway Tools Software in 2009
Pathway Tools is a production-quality software environment for creating a type of modelorganism database (MOD) called a Pathway/Genome Database (PGDB). A PGDB such as EcoCyc integrates the evolving understanding of the genes, proteins, metabolic network, and regulatory network of an organism. This article provides an overview of Pathway Tools capabilities. The software performs multiple computa...
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Ovarian carcinoma immunoreactive antigen-like protein 2 (OCIAD2) is a protein with unknown function. Frequently methylated or downregulated, OCIAD2 has been observed in kinds of tumors, and TGFβ signaling has been proved to induce the expression of OCIAD2. However, current pathway analysis tools do not cover the genes without reported interactions like OCIAD2 and also miss some significant gene...
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ژورنال
عنوان ژورنال: Standards in Genomic Sciences
سال: 2011
ISSN: 1944-3277
DOI: 10.4056/sigs.1794338