Searching Artifacts

A query sequence that contains repetitive elements is likely to produce many false and confoimding database matches. One clue that this may be a problem is the 

Sequences producing High-scoring Segment Pairs  

A program called seg has been developed to partition a protein sequence into segments of low and high composihonal complexity (Wootton and Federhen, 1996 Wootton and Federhen, 1993). Using this program, it has been shown that more than half of the proteins in the database contain at least one LCR (Wootton, 1994 Wootton and Federhen, 1993). The evoluhonary, fimchonal, and structural properties of LCRs 

In DNA, there are many classes of satellite and microsatellite sequences that consist of many copies of a simple repeat unit. 

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Optimization should be viewed as a tool to aid in decision making. Its purpose is to aid in the selection of better values for the decisions that can be made by a person in solving a problem. To formulate an optimization problem, one must resolve three issues. First, one must have a representation of the artifact that can be used to determine how the artifac t performs in response to the decisions one makes. This representation may be a mathematical model or the artifact itself. Second, one must have a way to evaluate the performance—an objective function—which is used to compare alternative solutions. Third, one must have a method to search for the improvement. This section concentrates on the third issue, the methods one might use. The first two items are difficult ones, but discussing them at length is outside the scope of this sec tion. 

Even with everything under control, an analyst is well-advised to keep his eyes open so he will have an idea of what artifacts could turn up, and can plan to keep irregularities in check. The list of items in Table 4.44 could turn up in the checklist of any GMP-auditor worth his salt a corresponding observation would probably trigger his suspicion that there might be further weak spots. The table is given here to provide the reader with an idea of the human and technical factors that can influence the quality of results, and to permit a search for examples that fit a certain category. 

Coins and artifacts of the Roman Empire have been studied extensively (4, 5, 19-39), but a thorough search of the literature indicates these small, copper coins of the Herodian King Agrippa have been omitted from all previous examinations. The iconography of die coins in this sample set is crude, but all have at least a recognizable wheat ear side or an umbrella side. A worn state or... 

Several note vorthy halogenated terrestrial alkaloids are known, with epibatidine (104) at the top of the list [88]. This apparent frog Epipedobates tricolor) metabolite has powerful analgesic activity [89] and an intensive search is underway for a clinically useful drug [90]. A few chlorinated plant alkaloids have also been discovered. Romucosine F (lOS) is present in Annora purpurea, a South American bushy tree [91], and the closely related romucosine B (106) is found in the stems of RolUnia mucosa [92]. The furoquinoline alkaloid chlorodesnkolbisine (107) was isolated from the African folk medicine plant Teclea nobilis [93]. The authors of this latter study provide convincing evidence that 107 is not an isolation artifact (e.g. from the corresponding epoxide with HCl). 

The study of obsidian provenance differs from that of pottery. As compared with clays, there are a lot fewer obsidian sources hence the search for chemical matches with artifacts is much simpler. The composition of obsidian is not altered in fashioning implements, whereas potters can refine a clay in different degrees, introduce additives, or blend different clays. Experience shows that obsidian flows are more uniform in composition than are clay beds therefore, the chemical profiles are more distinctive for obsidian. 

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