Database search tools

ProteinProspector (http //prospector.ucsf.edu), database search tools, searching by peptide mass, with MS/MS or Edman data, etc. 

This chapter is informally divided into two parts. The first part is devoted to sequence comparisons and culminates in the database search tool BLAST. The second part considers the analysis of population-level data, providing sufficient background to understand how genes influencing traits such as response to toxicity may be located within the genome. 

Lost in the above discussion is an unfortunate truth Even with DP, it takes too long to rigorously align a query sequence to each of the member sequences of a database. Because of this, database search tools seek approximations to the optimal local alignment, negotiating a balance between quality and speed with each comparison. This tradeoff and its implications are central to forthcoming discussion of the database search tool BLAST hosted at NCBI. 

The avaHabHity of citation searching tools is on the increase. A citation database for U.S. patents was first built by Search Check, Inc., which coHected aH U.S. patent citations back to their first appearance on patent copies in 1947. This database was subsequentiy made avaHable for on-line... 

In addition to addressing the practicalities of database maintenance, we also aim to enhance the range of the facilities available, to make the information within CHIRBASE more readily accessible to users. CHIRBASE contains two form-based applications for query building designed to help novice or expert users to formulate queries the query menu and the automatic search tool. 

Besides sensitive methods for the analysis of proteins, bioinformatics is one of the key components of proteome research. This includes software to monitor and quantify the separation of complex samples, e.g., to analyze 2DE images. Web-based database search engines are available to compare experimentally measured peptide masses or sequence ions of protein digests with theoretical values of peptides derived from protein sequences. Websites for database searching with mass spectrometric data may be found at http //www.expasy.ch/tools, http //prospector.ucsf. edu/ and http //www.matrixscience.com. 

ToxSeek is an NLM metasearch engine and clustering tool that enables the simultaneous searching of many different toxicology and environmental health information databases and web sites. This tool includes 59 databases including the TOXNET Search tool, as well as information sources from NLM, NIH, US Government, International and other sources. 

A number of recent examples of the use of pharmacophores as a primary VS method have appeared in the literature. Table 3 provides a selection of these studies, with outcomes listed. The databases searched range in size from 630 molecules to 1.7 million molecules. Of the studies shown in Table 3, the Catalyst software is the method most often used, followed by UNITY and the FlexS superposition tool. 

Gelbart WM. Databases in genomic research. Science 1998 282 659-661. Multiple authors The 2001 Database Issue. Nucleic Acids Res 2001 29 Altschul SF et al. Basic local alignment search tool. J Mol Biol 1990 215 403-410. 

PSI-BLAST (Altschul et al., 1997) is rapidly becoming the tool of choice for protein database searching because of its speed, sensitivity and ease of use. It presents a very large improvement over the older versions of BLAST and new gapped-BLAST implementations (Altschul et al., 1997 Altschul et al., 1990). However, a naive user can easily be misled or not get the best possible results. PSI-BLAST is available as a stand-alone program from ftp //and as an interactive web tool at http //www.ncbi. nlm.nih.gov/cgibin/BLAST/nph-psi blast... 

PubMed was developed by the National Center for Biotechnology Information (NCBI) at the National Library of Medicine (NLM) at the National Institutes of Health (NIH). The PubMed database was developed in conjunction with publishers of biomedical literature as a search tool for accessing literature citations and linking to full-text journal articles at Web sites of participating publishers. Publishers that participate in PubMed supply NLM with their citations electronically prior to or at the time of publication. 

An important aspect of our AI application is the attention paid to including well-established Fortran programs and database search methods into the decision structure of an expert system network. Only certain AI software tools (such as TIMM) effectively handle this critical aspect for the analytical instrumentation field at this time (57-60)> The ability to combine symbolic and numeric processing appears to be a major factor in development of multilevel expert systems for practical instrumentation use. Therefore, the expert systems in the EXMAT linked network access factor values and the decisions from EXMATH, an expert system with chemometric/Fortran routines which are appropriate to the nature of the instrumental data and the information needed by the analyst. Pattern recognition and correlation methods are basic capabilities in this field. 

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. 

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. 

At this moment, the NIST Chemistry WebBook and the Beilstein are the two most useful search tools for molecular structure and property relations. There are many more types of properties available in the research literature of interest only to a smaller set of readers these will not be listed in the general-purpose handbooks, but are to be found in specialized books and journals. Our ability to search for such properties in the research literature on the Internet is increasing rapidly, and students should practice doing such searches. Many of the required properties have not been tabulated in a searchable electronic database for example, flammability, toxicity, ozone hole potential, and greenhouse gas potential. Information on health, safety, and the environment that is publicly available on websites is listed in the references. 

The Explore view is useful to see some of the major categories available in your database, but with over 70,000 available parts, we need to use the search tools available in Capture CIS. 

MDL s Chemscape Server and Chime Pro product suite is an integrated set of tools for chemical structure illustration, communication, and database searching. Chime and Chime Pro are chemical structure visualization programs that run in the most popular Web browsers. 

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