ABT 104 Lecture 1st Exam

• Bioinformatics - “the application of computational tools to organize, analyze, understand, visualize and store information associated with biological macromolecules” (Luscombe et al, 2001)
• Bioinformatics studies provide methods and tools

  for analyses of genomic and proteomic data. (Zhang and Liu, 2013)
• Database - A collection of information stored in a systematic

  way, organized according to their function, or according to the species from which they came
• DNA, RNA, and protein sequences - The sequence of nucleotides in DNA or RNA, and the sequence of

  amino acids in a protein, can be obtained through

  laboratory sequencing methods.
• Molecular Structures - Higher molecular structure can be obtained by combining thermodynamic data and

  computer modeling with measurements from laboratory

  techniques, such as x-ray diffraction
• Expression Data - Scientists use microarrays in the laboratory to determine when and where genes are

  expressed. Such microarrays can also measure overall

  gene expressions in certain cell types, or in specific

  environmental conditions.
• Applications (APPS GC C)

  • Agriculture
  • Protein function analysis
  • Personalized medicine
  • Gene therapy
  • Drug development
  • Comparative Studies
  • Climate change studies
  • Structure-based medication outline
• How DNA Sequence Data is Obtained for Genetic Research

  Obtain Samples - Extract DNA and Sequence DNA - Compare DNA Sequences to One another
• Primary databases

  • DNA Data Bank of Japan (National Institute ofGenetics)
  • EMBL (European Bioinformatics Institute)
  • GenBank (National Center for BiotechnologyInformation)
  • NCBI
• Protein databases

  • Pfam: protein families database of alignmentsand HMMs (Sanger Institute)
  • PROSITE: database of protein families anddomains
  • Swiss-Prot: protein knowledgebase (SwissInstitute of Bioinformatics)
  • NCBI: protein sequence and knowledgebase (National Center for Biotechnology Information)
• RNA databases

  • Noncode – general sequence database
  • miRBase: the microRNA database involved in gene regulation
  • Rfam: a database of RNA families
  • SILVA – rRNA database