GENE 4: Comparing the genome Flashcards
Name two genome browsers
UCSC and Ensembl
How do you define genomic position for UCSC and Emsembl
Genomic position is defined as: chr:start-end
e.g. chr3:36993332-37050918
this defines the region between the 36993332th and the 37050918th nucleotide on chromosome 3
Except for displaying linear sequence of DNA what can genome browsers show?
Annotated genes
Transcript isoforms
CpG rich islands
What is the purpose of UCSC and Emsembl?
To calculate the similarity of genomic sequences between species
Similar sequences in the genome between species are known as?
Orthologs
What does ‘Cons 100 Verts’ determine?
It is the 100 vertebrates basewise conservation by phyloP and its a track that shows a histogram denoting the degree of conservation across different species
What does alignment mean?
A match between two sequences: these can be exact matches or have a few mismatches or gaps
What is BLAST used for?
Computational analysis of sequences alignments. It can determine whether there will be off-target effects of a homology-based molecular tool (e.g. PCR primers or CRISPR gRNAs)
Give two names of tools used for alignment analysis
BLAST and CLUSTAL omega
What is CLUSTAL omega used for? What do results show?
alignment of multiple genomic sequences that are input. If all input sequences have an identical base, it is denoted by an asterisk(*), if there are gaps they are denoted by a dash (-)
What are the features of optimal alignment?
- Most bases matching
- fewest gaps
- smallest gaps
- fewest mismatches
What was found when comparing the DNA of mice, humans, fruit fly and yeast using CLUSTAL?
Some regions are identical across the four genomes
Why were conserved regions not seen within introns in yeast?
Yeast genome do not have introns
What do conserved sequences between species suggest?
That there must be a reason they have remained unchanged in the millions of years of evolution and genetic variation. Sequences which are highly conserved include protein-coding sequences and regulatory regions, such as enhancers.
Why are phylogenetic trees generated?
To examine the relationships between the species and estimate their branch-points in evolution
What tool can be used to upload an alignment file to determine the phylogenetic relationship between species?
EBI simple phylogeny
What does EBI simple phylogeny data show?
Distances between the species represents the differences between them. Thus, looking at the tree we can see that Human and Mouse are related closely and that the Fruit fly sequence diverged from mammalian.
What do mechanisms of genetic change mostly involve?
Base substitutions and structural rearrangements that are mostly deleterious resulting in an organism less-suited to its environment.
Name the different types of genetic mutations
deletion duplication translocation insertion inversion substitution
What is the most common mechanism of genomic change?
Recombination which occurs during prophase I
Give 3 reasons why recombination is a successful way of introducing genetic diversity
- Parental chromosomes came from organisms able to survive to reproductive age thus incorporating changes between them is unlikely to be deleterious
- By occurring in germ cells, the changes can be passed to future generations
- No risk of random mutation
Why does recombination not occur in cells in prophase for mitosis?
Differences in chromosome shape
Explain why recombination is able to occur during prophase I, name the proteins holding the chromosomes together
Meiotic chromosomes form denser structures and line up as bivalents allowing all 4 copies of a gene to align. The maternal and paternal chromosomes are held together by the cohesion complex following replication. The maternal and paternal chromosomes are held to each other at branch points, known as chiasmata, wherein recombination can occur.
What happens with the chromosomes for people with down syndrome?
Chromosome 21 does not segregate properly resulting in a zygote with an extra chromosome 21
