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transcripts and proteins

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tools update

BACKGROUND: The recent flood of data from genome sequencing and functional genomics has given rise to new field, bioinformatics, which combines elements of biology and computer science. OBJECTIVES: Here we propose a definition for this new field and review some the research that is being pursued, particularly in relation to transcriptional regulatory systems. METHODS: Our definition is as follows: Bioinformatics is conceptualizing biology in terms of macromolecules (in the sense of physical-chemistry) and then applying "informatics" techniques (derived from disciplines such as applied maths, computer science, and statistics) to understand and organize the information associated with these molecules, on a large-scale. RESULTS & CONCLUSIONS: Analyses in bioinformatics predominantly focus on three types of large datasets available in molecular biology: macromolecular structures, genome sequences, and the results of functional genomics experiments (eg expression data). Additional information includes the text of scientific papers and "relationship data" from metabolic pathways, taxonomy trees, and proteinprotein interaction networks. Bioinformatics employs a wide range of computational topics including sequence and structural alignment, database design and data mining, macromolecular geometry, phylogenetic tree construction, prediction of protein structure and function, gene finding, and expression data clustering. The emphasis is on approaches that integrate a variety of computational techniques and heterogeneous data sources. Finally, bioinformatics is a practical discipline. We survey some representative applications, such as finding homologues, designing drugs, and performing large-scale censuses. Additional information pertinent to the review is available over the w...

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Basic local alignment search tool (BLAST) is a sequence similarity search program. The National Center for Biotechnology Information (NCBI) maintains a BLAST server with a home page at

Kleisli is a modern data integration system that has made a significant impact on bioinformatics data integration. This paper contains a brief introduction to the Kleisli system and an example to illustrate its uses in the bioinformatics arena. The primary query language provided by Kleisli is called CPL, which is a functional query language whose surface syntax is based on the comprehension syntax. Kleisli is itself implemented using the functional language SML. So this paper also describes the influence of functional programming research that benefits the Kleisli system, especially the less obvious ones at the implementation level. Availability. Kleisli has been commercialized under the name "KRIS". It is available from Kris Technology Inc., 713 Santa Cruz Ave, #2, Menlo Park, CA 94025. Direct email to info@kris-inc.com and web browser to http://www.kris-inc.com. 1 Introduction The Kleisli system (Davidson et al., 1997) is an advanced broad-scale integration technology that has pro...

The Rat Genome Database (RGD)