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