Databases finding sequences

In order to trace (find, change, add, or delete) a segment in the database, the sequence in which the data arc read is important. Thus, the sequence of the hierarchical path is parent > child > siblings. The assignment of the data entities uses pointers. In our example, the hierarchical path to K is traced in Figure 5-fi. 

The GENEMAN application is a tool that allows you to access and search for DNA and protein sequences located in six different biological databases. The search for a sequence of interest can be made as broad or restrictive as desired, since there are 12 different fields (definition, reference, source, accession number, etc.) to choose from when the search is performed. In addition to performing database searches to find sequences of interest, GENEMAN allows you to search the database for sequences that share homology with the sequence of interest, or for entries that contain a particular conserved sequence. Any number of different DNA or protein sequences found in these databases can be isolated and stored as a sequence file for later analysis. 

Reaction schemes for making specific compounds from readily available starting materials or solving particular sjmthetic problems are commonly reported in the literature. It is therefore desirable that a reaction database system allow input and indexing of complete reaction schemes. A reaction database system should be able to search reaction schemes for sequences of reactions that satisfy a query. In addition, the search program should be able to link together individual reactions in a database to find sequences implicitly represented in a reaction database by identif3dng if the product of one reaction is the reactant of another. 

ORAC, there are literature precedents for conversion of a ketone to an oxime, Beckmann rearrangement of oximes and for hydrolysis of amides, but no such composite reactions. This simple example highhghts a general problem of searching reaction databases the need to be able to find sequences of reactions that satisfy a user s query, when necessary. 

It is also possible to extend this concept to cover the presence of more than one distinct segm pair in a pair of sequences (for example, if there are three MSPs present with scores of 40, and 50 then one can calculate the probabOity of finding three pairs with at least a score of by chance). The ability of BLAST to provide a quantitative significance of any match fou is a particularly useful feature of the program, which, with its continuing development a availability, has made it the most widely used method for sequence database searching. 

Set the task of discovering new, previously unknown druggable receptors, how would we go about it In particular, how would we find a GPCR The first step toward functional annotation of a new GPCR sequence usually involves searching a primary sequence database with pairwise similarity tools. Such searches can reveal clear similarities between the query sequence... 

The following is a list of Web sites that teadets may find useful. The sites have been visited at various times by one of the authots (RKM). Most ate located in the USA, but many provide extensive finks to international sites and to databases (eg, for protein and nucleic acid sequences) and onhne journals. RKM would be grateful if readers who find other useful sites would notify him of their URLs by e-mail (rmurray6745 rogers. com) so that they may be considered for inclusion in fumre editions of this text. 

The SWISS-PROT and TrEMBL ID lines differ in the first two parts of the ID line. The first part is the entry name "ANP NOTCO" in the case of the SWISS-PROT example and "Q12757" in the TrEMBL example. The entry name used in all SP-TrEMBL entries is always the same as the accession number of the entry. The entry name used in REM-TrEMBL is the Protein ID tagged to the corresponding CDS in the EMBL Nucleotide Sequence Database. To the right of the entry name you will find either "preliminary" (in the TrEMBL entry) or STANDARD (in the SWISS-PROT entry). The data class used in TrEMBL is always PRELIMINARY. That means that the data are thoroughly checked by a computer,... 

How does one go about finding all of the relevant proteins in a database once it has been decided to carry out an analysis of an entire protein family The simplest approach is to use similarity search software such as SSEARCH or FASTA (Smith and Waterman, 1981 Pearson and Lipman, 1988) or BLAST (Altschul et al, 1997) with the amino acid sequences of one or two well-known members of the family as queries. The problem is initially the same as that of identifying all proteins that are homologous to a family of proteins, although with some important practical differ-... 

It can be difficult if not impossible to find the domain structure of a protein of interest from the primary literature. The sequence may contain many common domains, but these are usually not apparent from searches of literature. Articles defining new domains may include the protein, but only in an alignment figure, which are not searchable. Perhaps, with the advent of online access to articles, the full text including figures may become searchable. Fortunately there have been several attempts to make this hidden information available in away that can be easily searched. These resources, called domain family databases, are exemplified by Prosite, Pfam, Prints, and SMART. These databases gather information from the literature about common domains and make it searchable in a variety of ways. They usually allow a researcher to look at the domain organization of proteins in the sequence database that have been precalculated and also provide a way to search new sequences... 

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