Regular expressions

Obviously the regularity expressed in the qualitative form (a) is far less informative than any one of the quantitative presentations, (b), (c), or (d). The relative merits of the expressions (b), (c), and (d) depend upon the use. Table l-II tells in most detail exactly how much is known about the pressure-volume behavior of oxygen gas (from this experiment). In the graphical presentation of Figure 1-8 the trend of the data is shown by the smooth curve drawn to pass near as many points as possible. Uncertainties caused... 

CYP1B1 (chromosome 5) has been linked to primary congenital glaucoma. CYP1B1 is not regularly expressed in liver but is often found in various kinds of tumours. It metabolizes retinoids and many aromatic amines and PAHs to potentially carcinogenic products. 

For each X the effective external potential A t is adapted such that the density always equals the density of the fully interacting system. Hence p(r) is independent of the actual value of X. Clearly, for X = 0, we recover the Hamilton operator for the non-interacting reference system, and V ° = Vs, while X = 1 is the regular expression for the real system... 

It must be emphasized that the duodectet rule (4.6) initially has no structural connotation, but is based on composition only. Indeed, the compositional regularity expressed by (4.6) encompasses both molecular species (such as the metal alkyls) and extended lattices (such as the oxides and halides) and therefore appears to transcend important structural classifications. Nevertheless, we expect (following Lewis) that such a rule of 12 may be associated with specific electronic configurations, bond connectivities, and geometrical propensities (perhaps quite different from those of octet-rule-conforming main-group atoms) that provide a useful qualitative model of the chemical and structural properties of transition metals. 

The majority of prosite documentation refers to motifs rather than profiles. The motifs are less sensitive than profiles and do not provide statistical scores. The motifs correspond to active sites and other important functional sites in proteins. The motifs are expressed as regular expressions that can be used to detect matching proteins in the database. An example of a motif from Prosite would be the /V-glycosylation motif,... 

Consider the domain of a six-membered ring with single unsaturation. Table 3 expresses the synthetic route with one substituent. Again, the symbol V represents an arbitrary substituent. Square brackets surrounding a set of symbols indicates optionality of those symbols (as in regular expression notation). For example, the string may reduce... 

General forms are easily developed for other reactions. The machinery introduced in this section can then be utilized to write disconnection rules for other reactions. For example, consider the Diels-Alder adduct bicyclo[2.2.1]hept-2-ene. Using the regular expression notation described previously, the line notation for these types of compounds can be represented as... 

To avoid such a problem, we make use of regular expressions. They can also be easily implemented with MySQL. Thus, if we are interested in... 

Quick search This is the fastest way to generate a query. Click the checkbox to select databank (s) — for example, EMBL for nucleotide sequences or SWISSPROT for amino acid sequences. Enter the query word(s), accession ID, or regular expression and then click the Go button to start the search. 

Oxl5 chemical activity of the oxidized part of redox (Reaction 1.1), regularly expressed in mole per cubic meter, usually in mole per liter... 

As for organisms, our class 10, Linnaeus had this sorted out in the 18th century with his Systema Naturae. With some modifications (these days you and I are H. sapiens rather than H. diurnus—II. nocturnus was the orangutan ), his binomial system has survived to the present day, and of course is eminently well suited to being mined out with a simple regular-expression-based system. The options for (slightly) more machine-readable identifiers are the NCBI Taxonomy and the Life Science Identifier (LSID) project (see the LSID resolver at http //lsid.tdwg.org/). 

Regular expressions specify a set of character strings and are useful for pattern matching. In the context of an MSA, regular expressions can be used to define,... 

There are other approaches to family databases that rely more extensively on sequence similarity to define classes of genes or proteins. For example, PROSITE (49) is a resource that uses regular expressions to define patterns of residues that represent biologically significant sequence motifs. Recent versions have incorporated profiles, weight matrices that express the characteristics of a gene... 

Arbitrary path definitions are to be supported, as motivated above. Similar to regular expressions, we plan to support basic operations like alternation and quantification of graph patterns in order to restrict the set of possible paths. Quantification is already realized by the concept of set-valued graph patterns (see below). 

Fig. 1. Converting a alignment of sites into a regular expression (RE) and a position weight matrix (PWM). The alignment of DNA sites is shown at the top. The RE (using the IUPAC ambiguity codes) is shown aligned below the sites. The corresponding counts of each letter in each alignment column—the position-specific count matrix (PSCM)—are shown in the next box. The PWM is shown below that. The last box shows the information content LOGO for the motif.

In computer science, textual patterns are often represented by regular expressions. 

A regular expression (sometimes abbreviated regex) is a way for a computer user or programmer to express how a computer program should look for a specified pattern in text and then what the program is to do when each pattern match is found (www.whatis.com). 

---