Molecular Evolution: Computer Analysis of Protein and by Abelson J.N., Simon M.I., Doolittle R.F. (eds.)

By Abelson J.N., Simon M.I., Doolittle R.F. (eds.)

This quantity addresses a number of parts during which desktops are used to control and manage nucleic acid and protein series information. The manipulations comprise looking out, aligning, and picking the importance of similarities, in addition to the development of phylogenetic bushes that convey the evolutionary heritage of comparable sequences. Ready-to-use equipment for the "at-the-bench" scientist are awarded.

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Additional resources for Molecular Evolution: Computer Analysis of Protein and Nucleic Acid Sequences

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Such a database may be highly redundant because. data from different sources often overlap. However, the data entries can be indexed, the nomenclature of molecules and organisms can be standardized, and the data entries can be ordered to facilitate the location of similar data. The “new data” file of the NBRF Protein Sequence Database and many of the entries in GenBank are examples of this type of data. An abstract database provides the research community with a comprehensive collection of sequences and associated annotations in a form that can be examined and manipulated by computer.

J. McLaughlin, W. C. Barker, and L. T. Hunt, Natunvissenschuften 62, 154 (1975). I2 M. 0. Dayhoff, W. C. Barker, and L. T. Hunt, this series, Vol. 91, p. 524. 38 DATABASES 131 superfamily organization is helpful in the interpretation of database searches inasmuch as, if a new sequence is truly homologous with one already in the database, it should show unusual sequence similarity to the corresponding regions of other members of the superfamily as well. Furthermore, it is possible to choose a representative subset of the database for searching by removing all sequences that are, for example, less than 20% different from another sequence.

In the context of the current sequential organization, this problem must be resolved by the unsatisfactory strategy of choosing one type of domain on which to base the superfamily assignment. Under the proposed scheme, although the entire multidomain protein will be shown in a regular entry, each domain can also be represented separately on an alignment of related domains. This new organization provides a flexible environment for depicting the interrelationships among sequences and subsequences.

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