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• Bioinformatics


  The field of science in which biology, computer science, and information technology merge into a single discipline
• Bioinformatics


  • The science of managing and analyzing biological data using advanced computing techniques
  • Its ultimate goal is to enable the discovery of new biological insights as well as to create a global perspective from which unifying principles in biology can be discerned
• Bioinformatics (term)


  Coined in 1970 by biologists and researchers Paulien Hogeweg and Ben Hesper to refer to the study of information processes in biotic systems
• What is done in bioinformatics


  • Analysis and interpretation of various types of biological data including: nucleotide and amino acid sequences, protein domains, and protein structures
  • Development of new algorithms and statistics with which to assess biological information, such as relationships among members of large data sets
  • Development and implementation of tools that enable efficient access and management of different types of information, such as various databases, integrated mapping information

  
• Why use bioinformatics


  • The considerable "algorithmic" complexity of biological systems requires a vast amount of detailed information at the cellular and molecular levels for their complete description
  • The need for systematic organization, and analysis, towards an integrated view of biology, dedicated to the computational "mining" or in-silico analysis of this experimental data
  • Availability of three-dimensional (tertiary) structure of any biomolecule (say a protein) is vital to understand its structure-function interactions at the molecular level, and to undertake any molecular design tasks
  • Application of bioinformatics tools allows for high-throughput analysis and theoretical experiments
• How is bioinformatics used


  • Application of computer software tools for creating computer databases (both genomic and proteomic databases)
  • Development of algorithms to utilize and manage these databases in knowledge-based analysis
  • Utilization of databases and computational methods in "structure prediction" methods
  • Use of (primary, secondary and tertiary) databases and "structure prediction" algorithms in the rational molecular design to be applied in particular fields

  
• Software and tools of bioinformatics


  • Database interfaces: Genbank, EM, BL, DDBJ, Medline, SwissProt, PDB
  • Sequence alignment: BLAST, FASTA
  • Multiple sequence alignment: Clustal, MultAlin, DiAlign
  • Gene finding: Genscan, GenomeScan, GeneMark, GRAIL
  • Protein domain analysis and identification: pfam, BLOCKS, ProDom
  • Patient identification/characterization: Gibbs Sampler, AlignACE, MEME
  • Protein folding prediction: PredicProtein, SwissModeler

  
• BLAST


  Basic Local Alignment Search Tool, an algorithm for comparing biological sequences information, such as amino acid sequence of different proteins or the nucleotides of DNA sequences

  
• BLAST


  • Used to identify library sequences that resembles the query sequences
  • Designed by Eugene Myers, Stephen Altschul, Warren Gish, David J. Lipman and Webb Miller at the NIH and was published in J. Mol. Biol. in 1990

  
• Uses of BLAST


  • Identifying species
  • Locating domains
  • Establishing phylogeny
  • DNA mapping
  • Comparison
• Kinds of BLAST


  • Nucleotide-nucleotide BLAST (blastn)
  • Protein-protein BLAST (blastp)
  • Position-specific iterative BLAST (PSI-BLAST)
  • Nucleotide 6-frame translation-protein (blastx)
  • Nucleotide 6-frame translation-nucleotide 6-frame translation (tblastx)
  • Protein-nucleotide 6-frame translation (tblastn)
• BLAST process


  1. Works through use of heuristic algorithm

  2. Finds homologous sequences by locating short matches between the two sequences (seeding)

  3. Locates all common words between the sequences of interest (query) and hit sequences (sequences from database)
• Smith-Waterman algorithm


  A well-known algorithm for performing local sequence alignment, more accurate but slower than BLAST
• FASTA


  A DNA and protein sequence alignment software package, with a focus on calculating accurate similarity statistics

  
• Fields of bioinformatics


  • Molecular biology
  • Medicine and pharmaceutical
  • Environment and agriculture
  • Molecular engineering and biotechnology
  • Forensics
• Applications of bioinformatics


  • Genome and protein sequencing
  • Structure prediction and molecular modeling
  • Crop improvement
  • Gene therapy
  • Research, design, and development of novel molecules
• The development of new mapping technologies, associated with the genome projects, has accelerated the pace of identification of disease genes, and the underlying principles of mutational mechanisms

  
• Building on the foundation of structural and functional genomics will provide information on the role of each gene
• Once a DNA sequence of a gene is known, one can attempt to unravel its functional significance

  
• Application of bioinformatics in vaccine development through reverse vaccinology accomplished within 1-2 years vs conventional process taking 5-15 years

  
• Challenges in bioinformatics


  • Lack of "bioinformaticians"
  • Explosion of information
  • High cost
• The recent enormous increase in biological data has made it necessary to use computer information technology to collect, organize, maintain, access, and analyze the data
• Computer speed, memory, exchange of information over the Internet has greatly facilitated bioinformatics
• The bioinformatics tools available over the Internet are accessible, well developed, fairly comprehensive, and relatively easy to use