Bioinformatics

• Define bioinformatics

  It is the use of computer technology to analyse biological data.
• Give some example uses of bioinformatics

  Genome sequencing.

  DNA identification.

  Protein structure.
• What is the input for genomics

  DNA
• What is an example use of genomics

  Whole genome sequencing
• What is the input for epigenomics

  DNA modifications
• What is an example use of epigenomics

  Whole genome sequencing using bisulfite.
• What is the input for transcriptomics 


  RNA
• What is an example of trancriptinomics

  RNA-seq
• What is the input for proteomics

  Proteins
• What type of omics use Mass spec

  Metabolomics and proteomics
• What is DNA barcoding

  It allows for species identification through a short section of DNA.
• Briefly describe DNA barcoding

  DNA is amplified using PCR and then sequenced.
• What technique is used in food fraud detection

  DNA barcoding
• What technique is used to identify pollens

  DNA barcoding
• What are the most commonly used data formats

  FASTA, GenBank, PDB, Newick and Clustal.
• What is FASTA format used for

  Nucleotide and amino acid sequences
• What is the sequence ID of this search

  NC_045512.2

  
• What format is this

  FASTA

  
• What is the first line called

  The definition line

  
• Waht is the text afer the sequence ID called

  The descriptor

  
• What is the text below the definition line called

  The sequence

  
• Which format has more information GenBank or FASTA

  GenBank
• Describe how FASTA data is generated

  The DNA is fragmented and then sequenced using a sequencer.
• What type of sequencing is used with FASTA


  Short read
• What is a query

  The input sequence
• What is the subject

  The sequence that the query is compared to
• What database is used to compare the composition of beef burgers

  BLAST
• What format are phylognetetic trees recorded in

  Newick
• What is phylogenetics

  The study of evolutionary relationships
• What is a clade

  A single ancestor and its descendants
• What does a branch of a phylogneetic tree show

  The passage of genetic information between generations. Longer lines indicate more divergence between generations.
• What technique is used to study the evolution of SARS-CoV2 variants

  Phylogenetic trees
• What is CLUSTAL format an example of

  Sequence alignment
• What is required to make a phylogenetic tree

  Sequence alignment
• What does * mean in CLUSTAL format

  That the sequence of amino acids or nucleotides is identical across all the sequences being compared.
• What does a gap or - mean in CLUSTAL

  There is no similarity of amino acids or nucleotides with the other sequences.
• Define sequence alignment

  Arranging amino acids or nucleotide sequences which allows you to identify regions of similarity.
• What is the primary key in a database

  This is the unique ID provided to an entry.
• What is accession number in a database

  The unique ID for the data entered.
• What are the two other names for Unique ID

  Accession number and primary key