Proteomic analysis 430 INDEX

The collecting, organizing, and indexing of sequence information into a database provides the scientist with a wealth of information on human genome and proteome. What makes this database so useful and powerful is its analysis, which may lead to information indicating that the sequence of DNA in question does not always constitute only one gene it may contain several genes. 

An important factor in the progress of bioinformatics has been the constant increase in computer speed and memory capacity of desktop computers and the increasing sophistication of data processing techniques. The computation power of common personal computers has increased within 12 years approximately 100-fold in processor speed, 250-fold in RAM memory space and 500-fold or more in hard disk space, while the price has nearly halved. This enables acquisition, transformation, visuahsation and interpretation of large amounts of data at a fraction of the cost compared to 12 years ago. Presently, bioanalytical databases are also growing quickly in size and many databases are directly accessible via the Internet One of the first chemical databases to be placed on the Internet was the Brookha-ven protein data bank, which contains very valuable three-dimensional structural data of proteins. The primary resource for proteomics is the ExPASy (Expert Protein Analysis System) database, which is dedicated to the analysis of protein sequences and structures and contains a rapidly growing index of 2D-gel electrophoresis maps. Some primary biomolecular database resources compiled from spectroscopic data are given in Tab. 14.1. 

The lab-on-a-chip concept is undergoing a rapid development phase at present, in contrast with the maturity of many of the other technologies that are discussed in this book indeed, the Royal Society of Chemistry (UK) has started publishing a new journal with this very title (http //www.rsc.org/Publishing/Journals/lc/index. asp). Biennial reviews of this field (Reyes 2002 Auroux 2002 Vilkner 2004 Dittrich 2006) provide ample evidence that any attempt here to describe the current state-of-the-art would be rapidly out of date, so the main thrust will be focused on more fundamental concepts additional problems associated with interfacing such devices to mass spectrometry are discussed in Chapter 5. It should be mentioned that the current flurry of activity in this field has been driven mainly by applications to proteomics and other areas of modem molecular biology, rather than to trace quantitative analysis of small molecules some examples of the latter applications, of direct interest here, are also given in Section 5.2.3. 

We thank Sophia Kossida, Jason Comander, and Yonatan Grad for their helpful suggestions and discussion of the computational screen design and ScanACE and BLAST analysis. The databases used in this work are Flybase (http // www.flybase.org), WormBase (http //www.wormbase.org), and WormPD (http // www.proteome.com/databases/index.hlml). 

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