Bioinformatics Course

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Questions and Answers

What is the main purpose of Dot-plot in bioinformatics?

To compare two sequences to reveal similarities

What is the purpose of a Substitution Matrix in bioinformatics?

  • To visualize phylogenetic trees
  • To identify repetitive sequences in DNA
  • To determine the structure of biomolecules
  • To score sequence alignment based on genetic and evolutionary differences (correct)

Homology directly implies a common ancestor between proteins.

True (A)

PAM stands for ________.

<p>Point Accepted Mutations</p> Signup and view all the answers

What does PAMx represent in terms of mutations over time?

<p>likelihood of mutations for sequences which are X PAMs in time</p> Signup and view all the answers

PAM0 matrix represents constant mutation (nothing changing).

<p>True (A)</p> Signup and view all the answers

What is the biggest problem associated with the PAM250 matrix?

<p>It is not symmetrical. (C)</p> Signup and view all the answers

What is the scoring metric used in alignment to align sequences?

<p>Relatedness Odds Matrix (Rij)</p> Signup and view all the answers

The _ matrix is a logarithmic scoring matrix used to score alignments based on relatedness odds.

<p>Log-Odds</p> Signup and view all the answers

Match the following matrices with their descriptions:

<p>PAM matrices = Used for analyzing sequences with known evolutionary distances BLOSUM matrices = Based on local sequence alignment of conserved regions Log-Odds matrix = Used to score alignments based on relatedness odds</p> Signup and view all the answers

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Study Notes

Bioinformatics

  • Bioinformatics combines biology, computer science, and mathematics to analyze and interpret biological data
  • Involves the development of algorithms, statistical models, and analytical methods to understand biological systems

Biomolecular Building Blocks

  • Biomolecules: DNA, RNA, proteins, carbohydrates, and lipids
  • Sequences and structures of biomolecules are used to understand biological systems

Databases

  • Sequence databases: store DNA, RNA, and protein sequences
  • Structure databases: store 3D structures of biomolecules

Structural Bioinformatics

  • Involves the analysis and prediction of 3D structures of biomolecules
  • Uses computational methods and algorithms to analyze and predict structures

Sequences

  • Analysis: involves the study of sequence data to understand evolutionary relationships, function, and structure
  • Comparison: involves the comparison of sequences to identify similarities and differences
    • Pairwise sequence alignment: compares two sequences to identify similarities and differences
    • Multiple sequence alignment: compares multiple sequences to identify conserved regions and evolutionary relationships
    • BLAST: a algorithm used to compare a query sequence to a database of sequences

Phylogenetic Trees

  • Used to represent evolutionary relationships between organisms
  • Can be constructed using sequence data and other biological data

Biomolecular Modeling

  • Involves the prediction of 3D structures of biomolecules
  • Uses computational methods and algorithms to predict structures

Pairwise Sequence Alignment

  • Used to compare two sequences to identify similarities and differences
  • Can be used to identify conserved regions and evolutionary relationships
  • Dot-plot: a graphical representation of pairwise alignment
    • Reveals where the two sequences are similar and highly identical
    • Allows for the alignment of sequences
    • Can be used for genome, gene, and protein analysis

Substitution Matrix

  • Used to score the alignment of two sequences
  • Represents the probability of one amino acid changing into another
  • Examples: PAM, BLOSUM
    • PAM: based on the observed evolutionary relationships in primary structures
    • BLOSUM: based on local sequence alignment of conserved regions

Log-Odds Matrix

  • Used to score the alignment of two sequences
  • Represents the logarithmic odds of one amino acid changing into another
  • Derived from the substitution matrix
  • Examples: PAM, BLOSUM

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