BME435 BIOINFORMATICS

BIOINFORMATICS Section 1: Introduction and biological databases. Section 2: Sequence alignment. Section 3: Gene and promoter prediction. Section 4: Molecular phylogenetics. Section 5: Structural Bioinformatics Section 6: Genomics and Proteomics

Section 1: Introduction and biological databases 1- Introduction What is BIOINFORMATICS? Goal/Scope Applications Limitations New Themes

WHAT IS BIOINFORMATICS? Bioinformatics is an interdisciplinary reseach area at the interface between computer science and biological science. Increasingly popular field - There is a very high demand for bioinformaticians both in industry and in academia.

BIOINFORMATICS involves the technology that uses computers for Storage, Retrieval, Manipulation, Distribution of information related to biological macromolecules such as DNA, RNA, and proteins.

HOW BIOINFORMATICS DIFFERS FROM A RELATED FIELD KNOWN AS COMPUTATIONAL BIOLOGY? BIOINFORMATICS is limited to Sequence, Structural and functional analysis od genes and genomes and their corresponding products. COMPUTATIONAL BIOLOGY encompasses all biological areas that involve computation. E.g. Mathematical modelling of ecosystems Population dynamics, Application of Game theory in behavioral studies.

GOALS and SCOPE GOALS: Better understand the living cell How it functions at the molecular level. Solving functional problems using sequence and sometimes structural approaches has proved to be a fruitful endeavor.

SCOPE: Bioinformatics consists of two subfields: The development of computational tools and databases. The application of these tools and databases in generating biological knowledge to beter understand living systems.

Overview of various subfields of bioinformatics The applications of the tools fall into three areas: Sequence analysis, Structure analysis, Function analysis.

SOFTWARE DEVELOPMENT DATABASE CONSTRUCTION AND CURATION APPLICATIONS Structure Analysis Sequence Analysis Function Analysis Nucleic acid structure prediction Protein structure Classification comparison Genome comparison Phylogeny Gene & promoter prediction Motif discovery Sequence database Searching Sequence alignment Metabolic pathway modelling Gene expression profiling Protein interaction prediction Protein subcellular localization SOFTWARE DEVELOPMENT DATABASE CONSTRUCTION AND CURATION

APPLICATIONS BIOINFORMATICS having a major impact on many areas of biotechnology and biomedical sciences. e.g. Knowledge-based drug design, Forensic DNA analysis, Agricultural biotechnology.

LIMITATIONS Bioinformatics has a number of inherent limitations. Bioinformatics is by no means a mature field. Most algorithms lack the capability and sophistication to truley reflect the reality. Errors in sequence alignment, an affect the outcome of structural or phyligenetic analysis. Many accurate but exhausitive algorithms cannot be used because of the slow rate computation. Instead, less accurate but faster algorithms have to be used. IT IS A GOOD PRACTICE TO USE MULTIPLE PROGRAMS, IF THEY ARE AVAILABLE, AND PERFORM MULTIPLE EVALUATIONS. A MORE ACCURATE PREDICTION CAN OFTEN BE OBTAINED IF ONE DRAWS A CONSENSUS BY COMPARING RESULTS FROM DIFFERENT ALGORITHMS.

NEW THEMES There is no doubt that bioinformatics is a field that holds great potential for revolitionizing biological research in the coming decades. The field is undergoing major expansion. In addition to providing more reliable and more rigorous computational tools for sequence, structural and functional analysis. THE MAJOR CHALLENGE FOR FUTURE BIOINFORMATICS DEVELOPMENT IS TO DEVELOP TOOLS FOR ELUCIDATION OF THE FUNCTIONS AND INTERACTIONS OF ALL GENE PRODUCTS IN A CELL.