Bioinformatics Flashcards
What is bioinformatics?
Bioinformatics is an interdisciplinary field that combines biology, computer science, and statistics to analyze biological data, particularly genomic data, using computational tools and techniques.
What does bioinformatics typically involve in the context of agricultural microbiology?
Bioinformatics in agricultural microbiology involves studying bacteria, fungi, or viruses using molecular techniques to analyze genomic composition, transcriptomes, metabolomics, and microbiomes.
What is sequencing?
Sequencing is the process of determining the precise order of nucleotides (A, T, C, G for DNA; A, U, C, G for RNA) in a DNA or RNA molecule.
Describe Sanger sequencing.
Sanger sequencing uses labeled dideoxy nucleotides (ddNTPs) to sequence DNA. It involves PCR amplification, separation of fragments by gel electrophoresis, and visual reading of a chromatogram to determine the sequence.
What is the key advantage of Sanger sequencing?
Sanger sequencing provides accurate sequencing results for smaller DNA fragments (up to ~1000 bases) and is useful for confirming PCR products or genotyping.
What is next generation sequencing (NGS)?
Next generation sequencing refers to modern sequencing technologies that allow for high-throughput sequencing of millions of DNA fragments simultaneously, providing more comprehensive genomic data compared to Sanger sequencing.
Differentiate between short read and long read sequencing.
Short read sequencing generates sequences up to ~300 base pairs, providing high accuracy and throughput, whereas long read sequencing produces longer sequences (>1000 bp), which can span repetitive regions and complex genomes.
Name a market leader in short read sequencing.
Illumina is a prominent company in short read sequencing, known for its high-throughput and accuracy in sequencing DNA fragments.
What are the main advantages of long read sequencing?
Long read sequencing allows for sequencing of longer DNA fragments, enabling better resolution of complex genomic regions, structural variants, and direct RNA sequencing.
Describe how nanopore sequencing works.
Nanopore sequencing involves passing DNA or RNA through a protein nanopore, where changes in electrical current are used to detect the sequence of bases, allowing for real-time sequencing.
What applications does nanopore sequencing excel in?
Nanopore sequencing is useful for real-time field sequencing, detection of methylation patterns, and sequencing native RNA without prior conversion to cDNA.
How is sequencing used in diagnostics and surveillance?
Sequencing is crucial in diagnosing pathogens rapidly, identifying antimicrobial resistance, and discovering novel infectious agents, enhancing public health responses.
Explain the process of characterizing a pathogen using genomics.
Genomic characterization involves sequencing the pathogen’s genome, assembling the fragmented DNA into a complete or partial genome, and identifying genes related to virulence and antimicrobial resistance.
What is genomic epidemiology?
Genomic epidemiology uses genomic data to track disease outbreaks, determine transmission routes, and understand pathogen evolution by analyzing genetic variations among pathogens.
How does comparative genomics contribute to understanding pathogen virulence?
Comparative genomics compares genomes of different strains to identify genetic variations associated with differences in disease severity or virulence among pathogens.
