Fundamentals of Bioinformatics - Ogurtsov A.N. 2013

Foundations of Bioinformatics
Subject Matter of Bioinformatics
Goals and Objectives of Bioinformatics

The foundational principle of bioinformatics is that Biopolymers, such as nucleic acid and protein molecules, can be represented as sequences of digital characters. Furthermore, representing the monomers of Amino Acid and nucleotide chains requires only a limited set of alphabetical symbols.

This flexibility in analyzing Biomolecules using restricted alphabets has driven the successful emergence of bioinformatics. The development and functional power of bioinformatics largely depend on advancements in computer hardware and software. The most basic tasks in bioinformatics involve the creation and maintenance of biological information Databases.

The Scope of bioinformatics encompasses three main components:

1) creating databases that enable the storage and management of large biological datasets;

2) developing algorithms and statistical analysis Methods to determine relationships between database elements;

3) utilizing these tools to analyze and interpret various types of biological data—specifically DNA, RNA, and protein sequences, protein structures, Gene Expression profiles, and biochemical pathways.

The objectives of bioinformatics are as follows:

1. To organize data so that researchers can access up-to-date information stored in databases and add new entries as fresh insights are acquired.

2. To develop software tools and information resources that assist in data management and analysis.

3. To apply these tools for Data analysis and the Structure/127.html">Interpretation of Results in a way that yields biological meaning.

The tasks of bioinformatics involve analyzing information encoded in Biological Sequences, specifically:

✵ discovering genes within the DNA sequences of various organisms;

✵ developing methods to study the structure and/or function of newly deciphered sequences and corresponding RNA Structural domains;

✵ identifying families of related sequences and building models;

✵ aligning similar sequences and reconstructing phylogenetic trees to uncover evolutionary relationships.

In addition to the tasks listed above, another critical issue in bioinformatics must be mentioned, which is directly related to pharmaceutical biotechnology—identifying drug targets (see Section 6.6) and discovering promising lead compounds (so-called "leads") (see Section 15.3).

The Subject Matter of Bioinformatics is realized through the following activities.

1. Management and Processing of biological data; this includes its Organization, tracking, protection, analysis, etc.

2. Facilitating communication among scientists, projects, and institutions engaged in basic and applied biological research. Communication may involve email, file transfer, remote login, teleconferencing, and the establishment of networked information resources.

3. Organizing sets of biological information, documents, and literature, as well as providing access to them, along with search and retrieval capabilities.

4. Analysis and interpretation of biological data using computational methods, namely visualization, mathematical modeling, and the design of algorithms for the massively parallel processing of complex biological structures.