quiz 1 Flashcards
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What is bioinformatics?
Bioinformatics concerns the generation, visualization, analysis, storage, and retrieval of large quantities of biological information.
How has bioinformatics impacted biomedical research?
Bioinformatics has revolutionized biomedical research.
What must be done to raw biomedical data to derive meaningful information?
Raw data must be analyzed, annotated, reformatted, mostly automated using bioinformatics software, and graphically represented.
Define DNA sequencing.
DNA sequencing is the process of determining the order of nucleotide bases in a DNA molecule.
What is Sanger sequencing?
Sanger sequencing produces .ab1 files that can be analyzed by Chromas or Geneious.
Name three platforms used in next-generation sequencing (NGS).
- Illumina
- Ion Torrent
- PacBio
What type of file is produced by Oxford Nanopore sequencing?
The file produced is fast5.
What are assembly files in genomics?
Assembly files include contigs and scaffolds, stored in FASTA format, and annotation files that provide information on gene locations and functions.
What is genome mapping?
Genome mapping is the process of determining the physical location of genes and other genomic features on a chromosome.
What is structural genomics?
Structural genomics is the study of the three-dimensional structure of proteins and macromolecules encoded by an organism’s genome.
What techniques are used in structural genomics?
- X-ray crystallography
- NMR spectroscopy
- Electron microscopy
Define functional genomics.
Functional genomics is the study of the functional properties of genes and genomic elements.
What are some methods used in functional genomics?
- Gene expression profiling
- RNA interference
- Genome editing
What is comparative genomics?
Comparative genomics is the study of similarities and differences between the genomes of different organisms.
Name two prominent examples of genomic data projects.
- The 1000 Genomes Project
- The Cancer Genome Atlas (TCGA)
What is the approximate size of the human genome?
The human genome is approximately 3.2 billion nucleotides long.
What is GenBank?
GenBank is a huge repository run by the US National Center for Biotechnology Information (NCBI).
What is sequence alignment?
Sequence alignment is a method to compare two or more nucleotide or protein sequences to identify similarities and differences.
What is the difference between global and local alignment?
- Global alignment: compares highly similar sequences
- Local alignment: compares sequences of different lengths with high variability
What is genome assembly?
Genome assembly is the process of piecing together fragments of DNA sequences to reconstruct the complete genome of an organism.
What are the two types of genome assembly?
- De novo assembly
- Reference-based assembly
Define phylogenetics.
Phylogenetics is the study of the evolutionary relationships between organisms based on their genetic and morphological characteristics.
What is gene annotation?
Gene annotation is the process of identifying details such as gene locations, similarities, and associations with phenotypes.
What is functional annotation?
Functional annotation is the process of identifying the functions of genes or proteins by analyzing their sequence and interaction networks.
What are some applications of bioinformatics in drug discovery?
- Screening of chemical libraries
- Computer-aided drug design
- Drug development studies
What is personalized medicine?
Personalized medicine is an approach to treatment that considers individual differences in genetics, environment, and lifestyle.
What are some challenges in bioinformatics?
- Data storage and management
- Data integration and analysis
- Ethics and privacy
What is the role of machine learning in bioinformatics?
Machine learning can accelerate the analysis of large biological data sets but requires careful validation.
What is the purpose of the NCBI?
The NCBI provides access to a wide range of biological databases and resources.
What is UniProt?
UniProt is a comprehensive database of protein sequences and functional information.
What does KEGG stand for?
Kyoto Encyclopedia of Genes and Genomes.
What is Expasy?
Expasy is a resource offering bioinformatics tools and databases related to protein analysis.
What does NCBI stand for?
National Center for Biotechnology Information
NCBI provides access to various biological databases.
What is the purpose of the NCBI’s Entrez?
It serves as an interface between users and data, facilitating searches across multiple databases.
Entrez is the search engine used by NCBI.
List three resources that can be accessed through NCBI.
- GenBank
- PubMed
- UniProt
What type of information does the UniProt database provide?
Protein sequence and functional information.
UniProt is a collaboration among EMBL-EBI, SIB, and PIR.
What does PubMed cover?
A very large literature database covering all major journals of biology and medicine.
What are Medical Subject Headings (MeSH) used for in PubMed?
They are used to index queries for searching literature.
Fill in the blank: Gene names can often be considered a _______.
moving target
What is the official gene symbol for ‘kibra’?
WWC1
What is OMIM?
Online Mendelian Inheritance in Man
What types of records does OMIM contain?
- Human genes
- Human disorders thought to be genetic
- Associated phenotypes
How can you limit your search to only nucleotide sequences in NCBI?
Change the menu from ‘All Databases’ to ‘Nucleotide’.
What is Gene Ontology?
An approach to answer questions related to protein functions, locations, and associations.
What does the Gene Database at NCBI compile?
Information from numerous sources on a single gene.
What does the ‘Genomic context’ section display?
Adjacent genes portrayed as arrows on the chromosome.
What is the function of the ‘Genomic regions, transcripts, and products’ section?
It shows a map of exons of transcripts along with accession numbers.
True or False: The same laboratory can have multiple names for the same gene.
True
What is the significance of the symbols next to the OMIM record numbers?
- (+) Associated phenotype
- (#) Diseases where the gene defect is known
- (%) Mapped disorders where the gene is still unknown
- (*) For genes not associated with a phenotype
What website can be used to search published information on a gene using synonyms?
iHOP (information Hyperlinked Over Proteins)
What types of evidence can be found in Gene Ontology?
Various forms of data supporting or refuting scientific conclusions.
What can be customized in PubMed searches?
- Filter display options
- Hyperlinks
- Advanced search
- Exporting files
