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 numerous components within which desktops are used to regulate and control nucleic acid and protein series facts. The manipulations comprise looking, aligning, and deciding upon the importance of similarities, in addition to the development of phylogenetic timber that exhibit the evolutionary historical past of comparable sequences. Ready-to-use equipment for the "at-the-bench" scientist are offered.

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Many database searching methods select a predetermined number of top-scoring segments. If the database redundancy is high, the scores saved may correspond to a small number of overrepresented proteins (or nucleic acids). A partial solution to this problem is to increase the number of top-scoring segments saved, but the investigator will be required to examine large amounts of output and, as a result, may still miss the important relationships. The third type of database is the reference data compendium that normally includes only one “value” for each item of data or perhaps the range of values covered by sources considered reliable.

Moreover, the resource is operated by a group of scientists with many years of experience in the application and interpretation of sequence comparison methods. Thus, the PIR is a center providing not only the necessary facilities for protein identification but also practical guidance in the interpretation of the results of these methods. What Kind of Database? There are three types of sequence databases that can be useful to biological researchers (Lennart Philipson at an EMBL/NIH Workshop, “Future Databases for Molecular Biology,” February 25-27, 1987).

0. Dayhoff and published by the NBRF. In addition to all of the known protein (and nucleic acid) sequences, these volumes contained alignments of sequences, tables giving the amount of difference between sequences, and evolutionary trees for many groups of related proteins. Further, they included chapters on aspects of molecular evolution and methods of sequence analysis as well as many useful tables of related data such as hemoglobin mutants, enzyme active sites, rates of mutation acceptance in proteins, average amino acid percentage compositions for families of proteins, and mutation probabilities for amino acids.

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