Term
|
Definition
| genes/proteins that have similar sequence and are derived from a common ancestral sequence |
|
|
Term
|
Definition
homologs derived through speciation
human alpha-globin and chimpanzee alpha- globin |
|
|
Term
|
Definition
homologs derived through gene duplication
Human alpha-globin and human beta-globin |
|
|
Term
|
Definition
| genes with similar sequence due to convergent evolution (not common ancestry) |
|
|
Term
| What is homologus search? |
|
Definition
| matching a given sequence to other known genes or proteins in a database |
|
|
Term
|
Definition
| Basic Local Alignment Search Tool,used homology search tool |
|
|
Term
|
Definition
| E represents the number of matches expected at random when searching a database of a given size |
|
|
Term
|
Definition
| uses a faster algorithm based on 11-mers (=11 bases of DNA) or 4-mers (=4 amino acids) to find matches of: 95% or greater identity over 25 bases or more (DNA) 80% or greater identity over 20 amino acids or more (Proteins) |
|
|
Term
| What BWA, bowtie, Stampy, NextGenMap are used for? |
|
Definition
|
|
Term
| What is the strategy of reciprocal best hits? |
|
Definition
Gene A from species 1 is used for a BLAST search of the species 2 genome
Gene A’ from species 2 is then used for a BLAST search of the species 1 genome |
|
|
Term
| Does reciprocal best hits guarantee orthologous search? |
|
Definition
|
|
Term
| Why procariotic genomes are better studies? |
|
Definition
a) small genome (0.6-10 Mb, single circular chromosome)
b) little repetitive DNA (easier assembly)
c) no introns (easier gene prediction)
d) medical/economic importance (e.g.,
human pathogens) |
|
|
Term
| Two major domains of procariots |
|
Definition
|
|
Term
|
Definition
previously protein
-
encoding genes that have mutations that disrupt the ORF (insertion of stop codon or insertion/deletion that causes frameshift) |
|
|
Term
| Who has the smallest genome? |
|
Definition
| Mycoplasma. Their ancestors had many more genes |
|
|
Term
| Why the reduction of genome in mycoplasma occurred? |
|
Definition
| Obligate association with host this sues promotes genome reduction.Many genes involved in energy metabolism,amino acid and vitamin synthesis are lost. |
|
|
Term
|
Definition
| a) Selective advantage for smallness? No.b) b) Mutation pressure |
|
|
Term
| Selective advantage for smallness? |
|
Definition
-small changes in DNA content do not affect replication rate
-many pathogens retain non-functional pseudogene
-small genomes are not more densely packed than large (same amount of “spacer DNA”) |
|
|
Term
| Signs of mutation pressure |
|
Definition
-there is a bias towards deletions
-there is a bias towards AT mutations |
|
|
Term
| What is the protein, which helps hyperthermophiles to survive? |
|
Definition
Reverse gyrase is a large protein that is a fusion of two protein domains, helicase and topoisomerase. It introduces twists into double-stranded circular DNA and may help
prevent unwinding of DNA at high temperatures |
|
|
