Abstract
The technique of comparison and analysis of biological sequences is playing an increasingly important role in the field of Computational Biology and Bioinformatics. One of the key steps in developing the technique is to identify an appropriate manner to represent a biological sequence. In this paper, on the basis of three physical–chemical properties of amino acids, a protein primary sequence is reduced into a six-letter sequence, and then a set of elements which reflect the global and local sequence-order information is extracted. Combining these elements with the frequencies of 20 native amino acids, a ( 21 + λ ) dimensional vector is constructed to characterize the protein sequence. The utility of the proposed approach is illustrated by phylogenetic analysis and identification of DNA-binding proteins.
Highlights
In the task of comparison and analysis of biological sequences, choosing a type of DNA/protein representation is an important step
relative distance (RD) can be viewed as an integration of the information on three side chain properties: composition; polarity; and molecular volume—where composition is defined as the atomic weight ratio of hetero elements in end groups or rings to carbons in the side chain
94.47primary sequence into a six-letter sequence, which can be regarded as a coarse-grained description of the protein primary
Summary
In the task of comparison and analysis of biological sequences, choosing a type of DNA/protein representation is an important step. The usual representation of the primary structure of DNA is a string of four letters: A (adenine); G (guanine); C (cytosine); and T (thymine). This expression is called a letter sequence representation (LSR) or a DNA primary sequence. A protein primary sequence is usually expressed in terms of a series of 20 letters, which denote 20 different amino acids. It is difficult to obtain the information from the representation of a primary sequence directly. Various sequence representation techniques have been developed for encoding bio-sequences and extracting the hidden information
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