• The 21^st?Century has seen a tremendous?increase?in the amount of?biological data
  • This has been due to rapid advances in?DNA sequencing?and other technologies
• Developments in scientific research have been accompanied by?improvements in computing, enabling scientists to interpret complex biological data using bioinformatics applications
• Bioinformatics?is an?interdisciplinary field?that develops methods and software to help further our understanding of life by making sense of this data
  • Although many new bioinformatics applications are at the forefront of applied computing, most scientific research uses?standard tools and databases
• Data related to gene sequence, protein structure, gene expression or metabolites is curated, annotated and stored in databases such as?GenBank, NCBI, EBI, PDB
• A range of?open source software tools?is available to query this data

Sequence similarity

• If a scientist has an unknown DNA sequence, they can determine if it codes for a gene
• BLAST?(Basic?Local?Alignment?Search?Tool) search can compare the unknown DNA sequence to?all known gene sequences?in a particular database
  • BLAST?finds regions of similarity?between sequences
  • The search returns ‘hits’ which are the sequences most related to the search sequence (depending on the parameters set)
• There are?many variations of BLAST?that can be used for different analyses such as?protein sequences?or comparing multiple input sequences at once

Genetic variation and evolutionary relationships

• Scientists can?compare homologous gene sequences?between many organisms
  • Sequences are compared using an alignment tool such as?Clustal W?(there are many alternatives)
  • This aligns (stacks) the sequences based on similar regions so that?variable regions can be identified
• This determines the?degree of similarity?between organisms which?gives an indication of how closely related?the organisms are
  • There may be a?common ancestral origin?but in some organisms, the gene might have accumulated differences over times from random mutations
• Tree-like evolutionary diagrams (phylogenetic trees) can be constructed with software such as?PhyloWin?to show the?degree of relatedness?to a recent common ancestor
• Phylogenetic analysis?is useful for biological classification, conservation studies, forensics or molecular epidemiology which can help dictate public health policy
  • Variants?of highly infectious pathogens such as SARS-CoV-2 (a well-known coronavirus) can be identified using these techniques

Sequencing DNA to determine protein sequences

• The?genetic code?can be used to determine the?amino acid sequence?within a protein
  • This primary structure information can be used to predict?how proteins will fold?into their tertiary structure
  • This gives a greater level of understanding of?how a protein functions?or?interacts?with other proteins or molecules
• Such information can be used for a range of applications, such as?drug design?or?novel protein engineering?in synthetic biology