Bioinformatics Flashcards
What is transciptomics?
study of gene expression data
What is GenBank?
Large datasets of DNA sequence
What is in vivo?
traditional biological experiments within an organism
What is in vitro?
traditional biological experiments in an artificial environment
What is in silico?
On the computer
What is bioinformatics?
Application of computer science for the management and analysis of biological information
What are computers used for in bioinformatics?
GATHER biological data
STORE intelligently and efficiently
Provide TOOLS to allow extraction of meaningful biological information
MERGE information from several sources to increase understanding
What is a primary database?
information about e.g. DNA sequences
What is a secondary database?
contain results of analysis of primary resources e.g. sequence patterns or mutations
What are the three main nucleotide sequence databases?
GenBank (National Center for Biotechnology Information -NCBI)
EBI -EMBL (European Molecular Biology Laboratory)
DDBJ (DNA Data Bank of Japan)
What is easier to obtain protein or DNA sequences?
Protein sequences
What is UniProtKB
(Universal Protein Resource Knowledgebase) – Comprehensive catalogue of information about proteins.
What was the first protein to have its structure determined?
myoglobin
What is Protein Data Bank (RCSB PDB)?
a protein data bank that stores over 100,000 structures
How is bioinformatics used to annotate genomes?
identify genes, protein coding regions
predict structures and functions
True or False?
Bioinformatics is a new research tool which will replace the need for laboratory experiments in the future
False
Experiments will still be needed as proof
True or False?
A bioinformatics database is an archive or store of biological data
True
True or False?
This is a nucleotide sequence ACTRFCGTRECATCGNKL
False
Protein sequence
True or False?
Protein structures are more difficult to determine than protein sequences
True
What is BLAST?
commonly used bioinformatics tool for rapidly comparing new sequences with known sequences e.g. All known nucleotide sequences
What can you find out if you have the complete sequence of a gene?
Gene name, organism, complete gene + protein sequences
Information about protein’s function, structure, evolution
Even if you don’t have the complete sequence of the gene you can still find out stuff about it.
What can you find out and how?
function, evolution etc from looking at related sequences
Because similar sequences may
have similar structure and/or function
have evolved from common ancestor
What can use to find out more about the human genome?
http://www.genecards.org/
What is http://www.ensembl.org/ ?
A whole genome browser
“software system which produces and maintains automatic annotation on selected eukaryotic genomes”
Can browse genome at different levels: chromosome ->gene->exon->nucleotide
What is sequence alignment?
‘line up’ sequences so that similar features are in same columns
What are ClustalW2 and Clustal omega
Most commonly used multiple sequence alignment program
Can align DNA or protein sequences
Requires fixed format input e.g. file with sequences in FASTA format
What is shotgun sequencing?
copy DNA many times
chop each up into many random fragments
sequence each little piece (“read”)
assemble fragments where they overlap
What is functional annotation?
Finding out what genes are for by looking at what the proteins do
Why would you rather use bioinformatics over experimental approaches to research functional annotation of genes?
Bioinformatics is a scaled up automatic approach making it much faster
During functional annotations what should you find out about the proteins?
Are there related proteins? (BLAST search) – cautiously infer function from these
Search secondary databases (e.g. SMART) for functional domains
Predict 3D structure – help to determine function where sequences are only weakly related to known proteins
What can you use genome sequencing for from a single genome?
What is necessary for life?
Genes that control economically important traits e.g. crops
Personalised medicine
What can use genome sequencing for comparatively?
How have species evolved?
What makes humans unique? Only 1% of our genes have not been found in other species!
