Databases & tools, comparative genomics I
23 important questions on Databases & tools, comparative genomics I
Where are sequences stored?
Where are all databases crosslinked?
What are examples of genome browsers?
- Ensembl
- UCSC
- NCBI Genome Data Viewer
- RefSeq collection
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What are 4 sequence analysis tools?
- ORF mapping
- Secondary structure prediction
- Pattern recognition
- Sequence alignment
What is a method for secondary structure prediction?
What is sequence alignment?
What tool can you use for sequence alignment?
What are the different BLAST algorithms?
- BLASTP: protein - protein
- BLASTN: DNA - DNA
- BLASTX: translated DNA - protein
- TBLASTN: protein - translated DNA
- TBLASTX: translated DNA - translated DNA
What is comparative genomics based on?
- and that differences in DNA suggest differences in function and behaviour between cells, tissues and organisms.
What are examples of things that are studied in comparative genomics?
- Ape vs. human being
- Cancer cell vs. normal cell
What is a phylogenetic tree?
What does the molecular clock describe?
How can the molecular clock be calibrated?
- with other information on common ancestry (for example, fossil records)
How can cladograms be constructed?
What are two things that you assume when using the principles of parsimony?
- The neutral change rate is constant
- Neutral changes are most likely in the 3rd base of the codon
Why did Carl Woese analyse rRNA for constructing cladograms?
- The sequence has changed slowly because of the importance of the transcript
- Fairly large molecule, so a lot of space for change
Why did Carl Woese's tree need to be revised?
What do you assume when you use the method of homology transfer?
What is the C-value paradox?
How can genomes evolve?
- By sequence modification: mutations (SNPs)
- By genome structure modification:
- deletion
- duplication
- translocation
- inversion
What can be concluded when genomes of different organisms are compared with each other?
What happens with groups of genes with a similar function or that are involved in the same process in evolution?
Where can you find synteny between proteins?
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