Bioinformatics tools

The primary data of sequencing projects are DNA sequences. These become only really valuable through their annotation. Several layers of analysis with bioinformatics tools are necessary to arrive from a raw DNA sequence at an annotated protein sequences ... 

The above bioinformatic tools provide methods of determining differences or similarities in datasets. The next step is to incorporate metabolomic data with other expression information, including mRNA and proteins, to infer gene function. To accomplish this, metabolomic data sets must be integrated and correlated in a global maimer with genetic and enzymatic data, pathways assembled into systems, and... 

Beukers, M. W., Kristiansen, I., AP, I. J., and Edvardsen, I. (1999) TinyGRAP database a bioinformatics tool to mine G protein-coupled receptor mutant data. Trends Pharmacol. Sci. 20,475-477. 

It is only natural that, to date, bioinformatics tools contribute most to the analysis of amino acid sequences. Only a small amount of current sequence data is subjected to direct experimentation. The majority of amino acid sequences currently accessible in public databases have been derived by in silico translations of nucleic acid sequence data, despite the fact that amino acid sequencing was introduced historically long before nucleic acid sequencing. It is hard to predict the future of the experimental generation of primary data. Certainly, sequencing of nucleic acids continues to become cheaper and faster, and novel techniques may further enhance the production of data. DNA chips are already used to detect differences between very similar sequences other methods may generate DNA data even more efficiently. 

Each report incorporates interactive tutorials that demonstrate how bioinformatics tools are used as a part of the research process. Currently, all Coffee Breaks are written by NCBI staff.17 Each report is about 400 words and is usually based on a discovery reported in one or more articles from recently published, peer-reviewed literature.18 This site has new articles every few weeks, so it can be considered an online magazine of sorts. It is intended for general background information. You can access the Coffee Break Web site at the following hyperlink http www.nc bi.nlm.nih.gov/Coffeebreaty. 

Obviously, not all proteins known to interact with ubiquitin or ubiquitin-like domains contain one of the professional ubiquitin-interaction domains. RptS and Rpnl, two subunits of the proteasome that bind to ubiquitin and UbLs, respectively, do not belong to any of the classes described above. Most probably, a large number of uncharacterized proteins with high affinity and specificity for ubiquitin are still waiting to be discovered. The bioinformatical tools described in the early sections of this chapter will be instrumental for this task. 

ExPASy (Expert Protein Analysis System, www.expasy.ch) or the National Centre for Biotechnology Information (NCBI, www.ncbi.nlm.gov) websites. Both websites provide bioinformatics tools, links to sequence databases and extensive bibliographic resources. As an example of the wealth of information available on individual enzymes, at the time of writing a search based on nitrilase in the Entrez protein section of NCBI will recover more than 10000 references to nitrilase enzyme amino acid sequences. These can be rapidly screened online by organism, and the individual entries will have links to amino acid and gene sequence, relevant literature and information on protein features (such as conserved domains). 

DNA microarrays offer the advantage of sensitivity, flexibility in the choice of genes for analysis, and power of analysis if combined with appropriate bioinformatics tools. Using DNA microarrays, the expression of thousands of genes can be measured simultaneously and in a high-throughput manner. 

Probes can be antibodies, other binding proteins constructed from protein fusions, or even oligonucleotide aptamers. While completion of the Human Genome Project has enabled access to content for nuclide acid arrays, the content for protein arrays is largely based upon available antibody libraries. Thus, the commercialization of protein microarrays remains largely dependent upon both commercial and institutional providers of protein content. These providers must also permit access to the data-based protein annotations. These are necessary in order for the protein array to be useful as a bioinformatics tool. 

Fig. 4. Application of bioinformatics tools to 2D-DIGE data analysis. Proteome data consisting of the normalized spot intensity values are exported from the image analysis software and their correlation with clinicopathological data examined. Using informatics tools including clustering algorithms and machine-learning methods, a novel cancer classification based on proteome data is established, and key proteomic features and proteins corresponding to biomarker candidates are identified.

Bioinformatics tools can be useful in whole genome analysis for some of the following tasks ... 

Bioinformatics tools involving computer-based statistical analyses are essential for data management and analysis. When a complex biological sample containing thousands of different proteins is analyzed by multifaceted approaches, such as multidimensional protein identification technology, the identification of the proteins in the mixture is extremely complicated. Even multiple peptide identification methods, such as using both MS and... 

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