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Practical Bioinformatics

Practical Bioinformatics. By: Dr David P Kateete , Makerere College of Health Sciences. Bioinformatics. Molecular biology Flow/function of biological information (life) in living things (classical experiments) Bioinformatics

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Practical Bioinformatics

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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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