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Bioinformatics Essentials: Understanding Life at Molecular Level

Dive into practical bioinformatics with this comprehensive guide by Dr. David P. Kateete. Explore the flow of biological information in living organisms through classical experiments and computational aids. Learn about molecular biology fields, functional genomics, proteomics, and more. Understand the fundamental aspects of sequence analysis, reading frames, genome descriptions, and omics revolutions.

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Bioinformatics Essentials: Understanding Life at Molecular Level

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  1. Practical Bioinformatics By: Dr David P Kateete, Makerere College of Health Sciences

  2. Bioinformatics • Molecular biology • Flow/function of biological information (life) in living things (classical experiments) • Bioinformatics • Flow/function of biological information (life) in living things (using computation aids—in silico)

  3. Molecular biology

  4. Fields in Bioinformatics • Bioinformatics • Creation, advancement of databases, algorithms, computational and statistical techniques and theory to solve formal and practical problems arising from the management and analysis of biological data. • Functional Genomics • Sequencing and comparative study of genomes to identify gene and genome functionality • Transcriptomics • Generating transcripts from genes: not all genes are transcribed!!! • Proteomics • Prediction of proteins from sequences, construction of pathways • Metabollomics/pathways • The “Omics” revolution

  5. Genome • Total description of entire DNA content of organism • Prokaryote: Chromosomal, extrachromosomal (plasmid); phage and MGE • Eukaryote: Chromosomal, extrachromosomal (mitochondrial); and MGE • <30% coding for genes • Junk/selfish DNA (70%)

  6. Junk/Selfish DNA • Repeat elements: • Satelite DNA---Micro/Mini satelite----Evolutionary studies • MIRU-VNTR—MTB typing • LINES/SINES: Retro elements, origin of retroviruses

  7. Practical Bioinformatics • Fundamentals of sequence analysis • Public sequence databases • Introduction to Blast services • The KEGG database

  8. Fundamentals of sequence analysis Reading Frames • Frame 1 (ORF) ATG CGC ACG GCC GCC GTC GGC CAC CAG TGC GTG • Frame 2 A TGC GCA CGG CCG CCG TCG GCC ACC AGT GCG TG • Frame 3 AT GCG CAC GGC CGC CGT CGG CCA CCA GTG CGT G

  9. Fundamentals of sequence analysis • Start codon: • ATG, • GTG • Stop codon: • TAG, • TAA, • TGA • Promoter sequence (the TATA box) • Shine Dalgano Sequence • Introns, Exons • Motifs/domains • Nature of amino acids: • hydrophillic, • aliphatic, • hydrophobic, etc

  10. ctcgaacgcgacggccgggtgagacaaatcagctcccatgtcttattcgtatgacacaggccactgatgtgtcaatgccacgttgcgcactaggctcggcgcggtgagcaccccgtacccgccgccaccgcctgcgcaggtcccgacgtgttatcggcatccggaccggccgacctacgtcagctgcacgcgttgccaccgcttcatctgcccggagtgcATGCGCACGGCCGCCGTCGGCCACCAGTGCGTGGACTGCGTCAACGCGGCCGCACGCACGGTGCCGGAGCCGCGCACCCGGTTCGGCGGCAAGGTCCGCGAGGGTGCCCCGGTGCTCACCTACACGCTCATCGCGGTCAACGTGCTGATGTTCGTGCTGCAGATCGCCGGAGGCGACCTGGAATCGCGGCTGACGCTGTGGCCGCCGGCGCTCGCGCTGCACGACGAGTACTACCGGCTGGTCACGTCGATGTTCCTGCACTACGGCGCGATGCACCTGCTGTTCAACATGTGGGCGCTCTACGTCGTGGGCCCGCCCCTCGAAAAATGGTTGGGGCTGACGCGATTCGGCGTGCTGTACGCACTGAGCGGACTCGGCGGCTCGGTGCTGGTGTACATGCTCTCGCCGTTGAACTCCGCGACGGCAGGCGCGTCGGGCGCCATCTTCGGCCTGTTCGGCGCGATCTTCGTGGTGGCCCGCCACCTCAACCTCGACGTGCGCGCGATCGGCGTGATCGTCGTGATCAACCTGGTGTTCACGTTCGTCGGCCCCGCTTTGGGAACCGCGATCAGCTGGCAGGGCCACATCGGCGGCCTGGTCACGGGTGCGCTGGTGGCATCGGCGTTCGTGTATGCCCCACGCGAGCGGCGCACCGCCACCGCGGCAGGGGTGACGGTCGCGTTCGCGATGCTGTTCGCCGCACTGATCTTCTGGCGAACAGACCGGCTGCTGTTCCTGCTCGGCGCAGGCTAGatcgccgcgcccggattcaggatgttgtccgggtccagcgcgcgcttgatccggtgattgagttccatggcgtccgggccgatctggttcgccagccacggccgcttgagccggccgacgccgtgctcgccggtgatggtgccgcccaggcccacggcgagttccatgatctcgccgaactcgaacgcgacggccgggtgagacaaatcagctcccatgtcttattcgtatgacacaggccactgatgtgtcaatgccacgttgcgcactaggctcggcgcggtgagcaccccgtacccgccgccaccgcctgcgcaggtcccgacgtgttatcggcatccggaccggccgacctacgtcagctgcacgcgttgccaccgcttcatctgcccggagtgcATGCGCACGGCCGCCGTCGGCCACCAGTGCGTGGACTGCGTCAACGCGGCCGCACGCACGGTGCCGGAGCCGCGCACCCGGTTCGGCGGCAAGGTCCGCGAGGGTGCCCCGGTGCTCACCTACACGCTCATCGCGGTCAACGTGCTGATGTTCGTGCTGCAGATCGCCGGAGGCGACCTGGAATCGCGGCTGACGCTGTGGCCGCCGGCGCTCGCGCTGCACGACGAGTACTACCGGCTGGTCACGTCGATGTTCCTGCACTACGGCGCGATGCACCTGCTGTTCAACATGTGGGCGCTCTACGTCGTGGGCCCGCCCCTCGAAAAATGGTTGGGGCTGACGCGATTCGGCGTGCTGTACGCACTGAGCGGACTCGGCGGCTCGGTGCTGGTGTACATGCTCTCGCCGTTGAACTCCGCGACGGCAGGCGCGTCGGGCGCCATCTTCGGCCTGTTCGGCGCGATCTTCGTGGTGGCCCGCCACCTCAACCTCGACGTGCGCGCGATCGGCGTGATCGTCGTGATCAACCTGGTGTTCACGTTCGTCGGCCCCGCTTTGGGAACCGCGATCAGCTGGCAGGGCCACATCGGCGGCCTGGTCACGGGTGCGCTGGTGGCATCGGCGTTCGTGTATGCCCCACGCGAGCGGCGCACCGCCACCGCGGCAGGGGTGACGGTCGCGTTCGCGATGCTGTTCGCCGCACTGATCTTCTGGCGAACAGACCGGCTGCTGTTCCTGCTCGGCGCAGGCTAGatcgccgcgcccggattcaggatgttgtccgggtccagcgcgcgcttgatccggtgattgagttccatggcgtccgggccgatctggttcgccagccacggccgcttgagccggccgacgccgtgctcgccggtgatggtgccgcccaggcccacggcgagttccatgatctcgccgaa

  11. Nature of amino acid MVIPVHDVNPVSRTPYVTYALIAANVFVFVFMPGLGSAPGDLSRLCHTQAFLEQYAAVPSELIRQQLPQLVPTGALAPSGGCALGPPGYDKSPALSVLTALFLHAGWLHLLGNMLFLLIFGTTIEDRLGRVRFALFYVACGYAASYGYAFVNADSTDPLIGASGAIAGVLGAYLVLYPRARVWVLVPFLVFLPLRLPAWLVLGFWFVLQAFNSSGEDALDVGTVAYAAHLVGFVAGMLLAWPLRPGTPPPPEPRGLLFGRRARPGW

  12. Public sequence databases • NCBI: USA • EBI: Europe • DDBJ: Japan • others • J Craig institute • Institute pastuer • The Sanger-wellcome trust center • The KEGG database

  13. Sequence alignments • Functionality • Phylogeny • Direction • Clustal W • MSCLE

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