Domains profile methods

The method can be used in combination with a multiple domain dissection procedure (Adams, et al., 1996) to construct a near full-length domain profile when the common domain is masked by the presence of other more conserved domains. 

One method for temporal precnrsor isolation is stored waveform inverse Fourier transform (SWIFT) [40]. In this method, the desired freqnency domain profile (all frequencies except that of the ion of interest) is inversely Fonrier transformed to a time domain waveform. This waveform is then applied to the excite electrodes in the ICR cell and, thns, the precursor ions are isolated in the cell. An alternative techniqne for in-cell isolation is correlated sweep excitation (COSE) [41], also known as correlated harmonic excitation fields (CHEF) [42]. This method involves application of radiofrequency pulses to the excite electrodes. The technique correlates the duration and frequency of the RF-pulses with those appropriate to the ions to be isolated. Both SWIFT and COSE are capable of isolating single isotopomers in peptide and protein ions [43-45]. 

More sophisticated methods that actually measure volumetric water content can also be used, such as time domain reflectometry (TDR). In Figure 14, an example of TDR results is presented. Both the calculated and measured (i.e., TDR) volumetric water contents provide a similar picture of the profile water status by depth with time. Proper soil characterization data, such as those shown in Table 6, are necessary for these calculations and improve understanding of the test system. The determination of water-holding capacity (WHC) at 0.03 MPa field capacity (FC) and 1.5 MPa... 

There is significant debate about the relative merits of frequency and time domain. In principle, they are related via the Fourier transformation and have been experimentally verified to be equivalent [9], For some applications, frequency domain instrumentation is easier to implement since ultrashort light pulses are not required, nor is deconvolution of the instrument response function, however, signal to noise ratio has recently been shown to be theoretically higher for time domain. The key advantage of time domain is that multiple decay components can, at least in principle, be extracted with ease from the decay profile by fitting with a multiexponential function, using relatively simple mathematical methods. 

The parsing of the transporter sequences into the TM domains shown in Fig. 1A represents the consensus result of three different methods. Average hydrophobicity was calculated with ProperTM using different window sizes and the Kyte and Doolittle scale (7). TMHMM, a hidden Markov model-based approach (8), and PHDHTM, a profile-based neural network method (9), were then utilized to refine the predictions. 

Another computational approach for detecting /1-solenoid sequences is implemented in a program called BETAWRAP (Bradley et al., 2001). This approach aims to identify /1-solenoid sequences by using hydrophobic-residue sequence patterns of strand-turn-strand regions that were learned from non-/l-solenoid structures. This method also takes into consideration the repetitive character of these patterns in /1-solenoids. Unlike the sequence profile approaches, BETAWRAP can make ab initio predictions of /1-solenoid domains. However, it is less sensitive than the profile search and, sometimes, cannot distinguish /1-solenoids from other solenoids (A. V. K, unpublished observation) such as, for example, LRR proteins (Kobe and Deisenhofer, 1994 Kobe and Kajava, 2001). The latest modification of BETAWRAP algorithm, which is called BETAWRAPPRO (McDonnell et al., 2006), employs additional data provided by sequence profiles and this improves the results of /1-solenoid predictions. 

Prosite is perhaps the best known of the domain databases (Hofmann et al., 1999). The Prosite database is a good source of high quality annotation for protein domain families. Prosite documentation includes a section on the functional meaning of a match to the entry and a list of example members of the family. Prosite documentation also includes literature references and cross links to other databases such as the PDB collection of protein structures (Bernstein et al., 1977). For each Prosite document, there is a Prosite pattern, profile, or both to detect the domain family. The profiles are the most sensitive detection method in Prosite. The Prosite profiles provide Zscores for matches allowing statistical evaluation of the match to a new protein. Profiles are now available for many of the common protein domains. Prosite profiles use the generalized profile software (Bucher et al., 1996). 

The SBASE database is a collection of annotated protein sequence segments (Murvai et al., 1999). SBASE avoids using consensus methods such as profile-HMMs and uses pairwise methods to detect domains. The database includes more than 130,000 annotated sequence segments that have been clustered into groups on the basis of BLAST similarities. SBASE currently contains 1038 domain families. 

Because of the preceding properties, our profile procedure appears to produce highly sensitive and specific common pattern representations from limited numbers of defining sequences compared with other current methods (Figs. 5 and 7). This was shown by the construction of such profiles from more than 50 completely unrelated functional families. In more than 90% of the families, the sensitivity and specificity are more than 98%. This is also supported by the repeated sampling study of the complex bacterial transcription initiation factors. Finally, these methods allow for the localized recognition of entire domains within multidomain structures, as seen in Fig. 6. 

The aforementioned properties make profile and HMM methods well suited for domain-detection purposes [8]. A large number of homology domains have been identified by each method, including several of the functional domains discussed below. 

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