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Bioinformatics quiz

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  • What is the main focus of bioinformatics?
    Bioinformatics focuses on studying genomic information to identify functional elements like genes, RNAs, and regulatory sites using databases and software.
  • What is genome annotation in bioinformatics?
    Genome annotation is the process of marking functional elements in the genome, such as genes and regulatory sites, often visualized with different colors and markers.
  • How do bioinformatics tools identify protein-encoding genes?
    They detect open reading frames (ORFs) that have characteristics of genes, such as 5' and 3' ends, introns, exons, and splice sites.
  • What is an open reading frame (ORF)?
    An ORF is a sequence in DNA that has features of a gene, including start and stop codons, and may contain introns and exons.
  • What is codon bias and how is it useful in bioinformatics?
    Codon bias is the preference for certain codons over others for the same amino acid, and it helps identify protein-coding regions in the genome.
  • How do fruit flies demonstrate codon bias for cysteine?
    Fruit flies prefer to use the UGC codon for cysteine, with 73% of cysteines encoded by UGC rather than UGU.
  • What is cDNA and how is it produced?
    cDNA is complementary DNA made from mRNA by reverse transcription, representing only the coding regions of genes.
  • Why is cDNA useful for confirming open reading frames?
    Because cDNA is derived from mRNA, it only includes expressed coding regions, confirming that an ORF is actually a gene.
  • What are expressed sequence tags (ESTs)?
    ESTs are short cDNA sequences collected in large datasets to show which genes are actively expressed in a cell at a given time.
  • How can bioinformatics predict DNA or protein binding sites?
    It searches for conserved sequences, such as promoters or splice sites, that are likely to be functional binding regions.
  • What is the proteome?
    The proteome is the complete inventory of all proteins encoded by an organism's genome.
  • What is a BLAST search and what is it used for?
    A BLAST search compares a nucleotide or protein sequence to databases to find similar sequences in other organisms, helping identify function and evolutionary relationships.
  • Where can you perform a BLAST search online?
    You can perform a BLAST search on the NCBI website.
  • How does bioinformatics help in evolutionary studies?
    It allows comparison of DNA or protein sequences across species to analyze similarity and evolutionary conservation.
  • What information can you obtain from a BLAST search result?
    You can learn which organisms have similar sequences and infer the possible function of the gene or protein.