Databases and Tools

General NCBI Entrez http //www.ncbi.nlm.nih.gov/ http //www.ncbi.nlm.nih.gov/Entrez/index.html Bioinformatics databases and tools. A cross-database searching system. 

NHGRI (National Human Genome Research Institute) http //research.nhgri.nih.gov/ microarray/main.html Protocols, databases, and tools... 

With the advancement of pharmacogenomics and systems biology research, more databases and tools should be available for various diseases. The application of these bioinformatics methods should assist us in having a more profound understanding of diseases at different levels and lead us to both individualized and systems medicine. 

Many of the bioinformatics programs contain redundant information, so we try to differentiate them based on their applications. Only some of those most commonly used tools are discussed because of space limitation. Web sites mentioned in this chapter were accessed in October 2007. The most recent advances in the field can be updated through browsing these sites regularly as new databases and tools are often added. To facilitate up-to-date bioinformatics support, an integrated search engine and updated collections of tools are freely available at http //sysmed.pharmtao.com. 

Barrett, T., Suzek, T.O., Troup, D.B., Wilhite, S.E., Ngau, W.C., Ledoux, P., Baidnev, D., Lash, A.E., Fujibuchi, W., and Edgar, R. (2005) NCBI GEO mining millions of expression profiles - database and tools. Nucleic Acids Res. 33 (Database issue), D562-D566. 

Large-scale gene expression studies, especially microarray technologies, have rapidly become a significant part of bioinformatics. There are many excellent sites focusing on microarray databases and tools for data analysis. The following sites are simply some examples. 

Database and tools pertaining to glycosylation pathways and glycosyltransferases. 

Barrett T, Suzek TO, Troup DB, Wilhite SE, Ngau WC, Ledoux P, Rudnev D, Lash AE, Fujibuchi W, Edgar R. NCBl GEO mining millions of expression profiles—database and tools. Nucleic Acids Res. 2005 33 D562-D566. 

In practice, these elements are often supported using available databases and tools. 

Bioinformatics databases and tools for epigenomics and microRNA studies ... 

Bioinformatics databases and tools for the studies of disease phenotypes and drug responses9... 

Shindyalov, I. N., Bourne, P. E. A database and tools for 3-D protein structure comparison and alignment using the combinatorial extension (CE) algorithm. Nucl. Acids Res. 2001,29, 228-229. 

CLiP provides a conceptualization of the most important entities and their relations in the domain of chemical process design. However, CLiP is not intended as a comprehensive, detailed product data model. Rather, it is understood as a conceptual model, based on which specialized implementation models can be developed, such as data schemata for domain-specific databases and tools, or neutral representation formats for the exchange of product data between heterogeneous software systems. Within the CRC, several implementation models for domain-specific software tools have been elaborated on the basis of CLiP. 

Chapter 2—Pattern Matching Using a variety of pattern-matching approaches is essential for any basic nucleotide sequence analysis and protein function determination. Markel and Rajapakse review the key motif, domain, and pattern databases and tools commonly used in drug target identification projects. 

We thank our customers and coworkers for their questions and requests that have given us the opportunity to explore many of the databases and tools described here. We also thank Darryl Leon for his careful review of this chapter. 

Since the databases and tools discussed in this book are unique in that they are freely shared amongst fellow academics, we would be remiss if we did not thank all of the people who, on a daily basis, devote their efforts to curating and maintaining the public databases, as well as those who have developed the now-indispensible tools for mining the data contained in those databases. As we pointed out in the preface to the first edition, the bioinformatics community is truly unique in that the esprit de corps characterizing this group is one of opeimess, and this underlying philosophy is one that has enabled the field of bioinformatics to make the substantial strides that it has in such a short period of time. 

C.-W. von der Lieth, NMR Databases and Tools for Automatic Interpretation of Spectra of Carbohydrates , in Bioinformatics for Glycobiology and Glycomics An Introduction, eds. C.-W. Von der Lieth, T. Luetteke and M. Frank, John Wiley Sons Ltd., Chichester, UK, 2009, p. 295. 

Provide for quick and easy linking of analysis tools. The set of analysis tools to be linked could involve such tools as COTS software (CAD, CAE, CAM), legacy (in house) codes, spreadsheets, databases, and tools to capture user s knowledge. 

ASTRAL Databases and tools for analyzing protein structure derived from SCOP http //astral.berkeley.edu/... 

Design representations, databases, and tools for disambiguation of descriptions and consistency checking are needed to support high-level synthesis. 

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