Bioinformatics. From Genomes to Drugs by Thomas Lengauer, Raimund Mannhold, Hugo Kubinyi, Hendrik

By Thomas Lengauer, Raimund Mannhold, Hugo Kubinyi, Hendrik Timmerman

Offers a wide, application-oriented assessment of this know-how. The cutting-edge in bioinformatics is evaluated both from a world view through introducing genuine software eventualities.

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Two modi®cations are required.

This is based on an automatic assignment of secondary structures for a given crystal structure followed by an assessment of the degree of accuracy of helix, sheet and loop predictions. As long as one restricts oneself to the problem of secondary structure prediction for a single sequence the limit in predicting accuracy today seems to lie around 63% [30]. PHD claims an accuracy up to 72% due to the inclusion of multiply aligned sequences. In practical applications, however, the concrete data set will decide about the success of secondary structure prediction.

In particular it implies that gaps at the ends are charged like any other gap. This, however, is a particularly unrealistic feature of a global alignment. 2), their respec- 37 38 2 Sequence Analysis tive N- and C-termini usually are dicult to match up and di€erences in length at the ends are more of a rule than an exception. Consequently, one prefers to leave gaps at the ends of the sequences un-penalized. This variant is easy to implement in the dynamic programming algorithm. Two modi®cations are required.

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