Search speeds

Finally we hope to see that more validation studies are conducted to compare any new search method with the reference exhaustive search (of course on a smaller validation virtual space of 104-106). Only through this type of rigorous validation studies, one can truly probe the rates of false positives and false negatives as well as the fold increase in search speed. This in turn allows end users to make informed decisions on which search method will be a best match for their specific tasks. 

Several of the above methods significantly increase the size of proteomic databases. This causes a decrease in peptide identification sensitivity (111,130), complicates protein inference (because of many redundant sequences) (160,161), and leads to longer search times. Although some efforts have been made to optimize search speeds (162), these hurdles remain unsolved. 

The default wordsize for a blastp search is three the default substitution matrix is the blosum62 matrix. Changing the wordsize from three to two increases the sensitivity of the search. Using a different substitution matrix can also have an effect on search sensitivity. During a blastp search, low-complexity regions of the query sequence are filtered to reduce the construction of spurious alignments and enhance search speed (see Note 4). 

Despite recent advances, the problem of spectral libraries size build-up, and search speed receives still considerable amount of attention. Most of the commercial databases to date use Fast Fourier Transform (FFT) for spectra compression. However, the past ten years have brought explosive growth of wavelet applications in signal processing. The IR spectra show many ab-... 

In order to perform a database search the structural key of the query molecule or substructure is compared with the stored structural keys of the database entries. This implies that each array element in the structural key has to be initially defined. Therefore, this key is inflexible and can become extremely long. The choice and number of patterns included in the key effects the search speed across the database. Long keys slow down searching, whereas short keys may screen out a lot of structures that are of no interest. On the other hand, this structural key can be optimized for the compounds present in the database to be investigated. 

Large-scale motions in proteins. The conformational search speed-up allows one to study large-scale motions in proteins and protein complexes. The use of the methodology to understand large conformational changes of the active site flaps in HIV protease [44] is a representative example it is unlikely that a comparable explicit solvent study would currently be computationally feasible. 

RealSpeak The RealSpeak system [108] was another significant landmark in that it was the first commercial unit selection system to be deployed. RealSpeak achieved yet further heights in terms of naturalness, and was showed that unit selection could be deployed in real time commercial systems, proof that practical constraints such as database size and search speed could be solved. Because of commercial acquisitions, today s (2006) RealSpeak has brought together ideas from many other systems, including the Speech Works system (itself a successor of the NextGen system), the Nuance system (a successor of Laureate) and rVoice, described below. 

Elsey, K. D. 1974. Influence of plant host on searching speed of two predators. Entomophaga 19 3-6. 

Table 3 Average Search Speeds for Each Component of a ChemDBS-3D Search.24 Speeds Are in Compounds per CPU Second on a VAX 8600...

The CSD is released, twice each year, as an indexed sequential binary file that contains additional data items derived from the basic input. Principally, these are bit-encoded screens that are required to enhance search speeds within the CSD software. Most screens are derived from the 2D connectivity... 

Perhaps the most significant feature of this virtual screen set is the incorporation of a rare and/or theoretical screen that is set when any generated fragment is not found in the "formal part of the screen fragment dictionary. The frequency of occurrence of this rare/theoretical screen is very rare. It can be viewed as a fail safe screen since it can logically complete any set of alternative screens for a synthetic screen without significantly detmorating the search speed. 

Research laboratories synthesize new compounds which are not contained in the library. In this second case, information about the structure of the new compound can be drawn from similarity searches, resulting in substructures assumed to be part of the query structure. The search algorithm is tuned to detect subspectra and the corresponding substructures. Techniques of this type can only be applied if structure-oriented databases exist. In the case of a similarity search the use of filter functions for accelerating the search speed is dangerous important information may be lost if relevant subspectra are filtered out. 

Most full-structure search systems use a hashing scheme to quickly locate potential matches and then perform a full lexical comparison of the name. A hashing function is used that takes the canonical name as input and returns a disk location to store and retrieve the name from. The number of hash collisions (where two different structures have the same hash value) is dependent on the hash function used and percentage utilization of the hash space. This database access method means that search speeds are relatively independent of database size, except where excessive hash collisions occur or numerous matches occur. 

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