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    Aula 1

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    Fundamentos de Bioinformática

    Ciências Biomédicas

    Faculdade de Medicina e Ciências Biomédicas


    Universidade do Algarve

    Clévio Nóbrega
    cdnobrega@ualg.pt
    • 1 – Introduction to Bioinformatics
    – Overview of bioinformatics and its applications in Biomedical Sciences
    – Introduction to biological databases (NCBI, Ensembl, UniProt)
    – Retrieving DNA and protein sequences from databases
    – Pairwise sequence alignment using BLAST
    Defining bioinformatics
    • The science of collecting and analysing complex biological data such as
    genetic codes – Oxford Languages

    • Bioinformatics, as related to genetics and genomics, is a scientific


    subdiscipline that involves using computer technology to collect, store,
    analyze and disseminate biological data and information, such as DNA and
    amino acid sequences or annotations about those sequences. Scientists and
    clinicians use databases that organize and index such biological information
    to increase our understanding of health and disease and, in certain cases, as
    part of medical care – National Human Genome Research Institute
    Bioinformatics

    https://proteomicsbioinformatics.wordpress.com/2018/07/25/bioinformatics/
    Why we need bioinformatics?
    • Human limitation in the ability to store and process data..

    – Example A: 2*48 = 96

    – Example B: 96*3234 = 310464


    Why we need bioinformatics?
    • These sequences are the same?

    1. ATGC
    2. ATGC
    Why we need bioinformatics?
    • And these ones?
    CCCGAGAAAGCAACCCAGCGCGCCGCCCGCTCCTCACGTGTCCCTCCCGGCCCCGGGGCCACCTCACGTT
    CTGCTTCCGTCTGACCCCTCCGACTTCCGAGGTCGAAACAGTAACAAAGGACTGCCTCAGTCTACGATTT
    CTTTTGATGGAATCTATGCAAATATGAGGATGGTTCATATACTTACATCAGTTGTTGGCTCCAAATGTGA
    AGTACAAGTGAAAAATGGAGGTATATATGAAGGAGTTTTTAAAACTTACAGTCCGAAGTGTGATTTGGTA
    CTTGATGCCGCACATGAGAAAAGTACAGAATCCAGTTCGGGGCCGAAACGTGAAGAAATAATGGAGAGTA
    TTTTGTTCAAATGTTCAGACTTTGTTGTGGTACAGTTTAAAGATATGGACTCCAGTTATGCAAAAAGAGA

    GAGTCAGATCTCGTTAGGATGGTTGTGAGCCACCATGTGGTTGCTGGGATTTGAACTCCAGACCTTCGGA
    AGAGCAGTCGGGTGCTCTTACTCACTGAGCCATCTCACCAGCCCGGTGGTTAGAATCTTTTGTGCTTGTG
    TTTTTCTGTCCTGCTAGATATGGGTGCTTGATGGGCGTCTTTTGTAGCACTTGGTGTCTTTAAGGGATTT
    GCAGGAAAGTAGACAGACTGGTATGATGACCCTTGAACACCTGCTACTTCAACACTTAGCAAGTCACACT
    GGTCTTGCTTCATATACCATCTATTTCCTTCTTCCTGTTACTCTGAAGCAGTGTAGAAGTTATTTTACGT
    GCAGGTTTTCTTGTGTTAATATAGCCAGCATTGTGTATAGGTGTGTGTGTGTGAGTGCACATGTGAGTAT
    Why we need bioinformatics?

    https://www.ncbi.nlm.nih.gov/genbank/statistics/
    Overview of bioinformatics and its applications in
    Biomedical Sciences
    1. Genomic Sequencing and Annotation:

    • Genome Assembly: Bioinformatics tools are used to assemble DNA sequences obtained from high-
    throughput sequencing technologies into complete genomes.

    • Gene Prediction and Annotation: Identification and annotation of genes within genomic sequences.

    2. Comparative Genomics:
    • Evolutionary Studies: Comparative analysis of genomes from different species to understand
    evolutionary relationships and identify conserved regions.

    3. Functional Genomics:

    • Gene Expression Analysis: Studying patterns of gene expression using techniques like microarrays
    and RNA-Seq.

    • Proteomics: Analyzing protein structures, functions, and interactions.


    Overview of bioinformatics and its applications in
    Biomedical Sciences
    3. Structural Biology:

    • Protein Structure Prediction: Computational methods to predict the three-dimensional structure of


    proteins.

    • Drug Design: Identifying potential drug targets and designing drugs by understanding molecular
    structures.

    4. Pharmacogenomics:

    • Personalized Medicine: Analyzing genetic variations to predict individual responses to drugs and
    optimize treatment plans.

    5. Disease Biomarker Discovery:

    • Identifying molecular markers associated with diseases, aiding in early diagnosis and prognosis.
    Overview of bioinformatics and its applications in
    Biomedical Sciences
    6. Disease Biomarker Discovery:

    • Identifying molecular markers associated with diseases, aiding in early diagnosis and prognosis.

    7. Systems Biology:

    • Studying biological systems as a whole, considering interactions between genes, proteins, and other molecules to
    understand complex biological processes.

    8. Metagenomics:
    • Analyzing genetic material directly from environmental samples, facilitating the study of microbial communities
    and their impact on health.

    9. Clinical Genomics:

    • Cancer Genomics: Analyzing genomic alterations in cancer cells to understand tumor biology and guide treatment
    decisions.

    • Diagnostic Tools: Developing bioinformatics tools for the interpretation of genetic tests and clinical sequencing
    data.
    Overview of bioinformatics and its applications in
    Biomedical Sciences
    10. Immunoinformatics:

    • Analyzing immune-related data to understand and predict immune responses, aiding in vaccine
    development and immunotherapy.

    11. Data Integration and Mining:

    • Integrating and analyzing diverse biological datasets to extract meaningful patterns and insights.

    12. Biological Database Management:

    • Creating and maintaining databases containing biological information, providing a centralized


    resource for researchers.

    13. Network Biology:

    • Analyzing and modeling biological networks, such as protein-protein interaction networks, to


    understand complex biological processes.
    Databases – an important component of
    bioinformatics
    Databases
    Databases – Scientific information: PubMed

    https://pubmed.ncbi.nlm.nih.gov/
    Databases – Scientific information: NIH

    https://ncbi.nlm.nih.gov/
    Databases – Information on genes

    https://www.ncbi.nlm.nih.gov/gene
    Databases – Information on genes
    Databases – Information on proteins

    https://www.uniprot.org/
    Databases – Information on proteins
    Databases – BLAST
    If I have a new sequence how to identify it or know the origin?

    DNA sequence
    Databases – BLAST

    https://blast.ncbi.nlm.nih.gov/Blast.cgi
    Databases – BLAST
    Databases – BLAST

    https://blast.ncbi.nlm.nih.gov/Blast.cgi
    Databases – BLAST
    Databases – BLAST: example
    > Unknown sequence
    GACTTGCCACTGAAGAGTGGCTGCTTGCAGGCTTGGCTTGCAGCTGGGGAGAGAGCATGAGCAGCGGCGG
    CGTCGGCGGCGGGAGCTTGGGCGCCGGCTTGCTGTACCACAAGTTCGTCAGCTTCGCGCTGGAGGAGACC
    CGACTCCGGACCACCCTCACCCCTCACCCCTCCCAGGAAAAGTTCAAGTCTATAAAACCCAATGATGATA
    ATACAGTTTTCAATGCTCTCTCATTCAGTGCACCGAAAATTAGATTGCTTCGCAGCTTGACAATCGAGAA
    GAAAAACTCATATCAGGTTCTTGACTTTGCCGCTTTCTCTGAACCTGAATACGATCTTCCTATATTTTGC
    GCCAACGTTTTTACAACTCATGCACAAAGTATTGTTGTATTGGACCTCAATCCTCTATATGATACTACAG
    In the classroom

    1. PubMed
    2. NCBI-Gene
    3. Uniprot
    4. Blast

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