Genomics

Question 1

what is genomics

Answer 1

study structure, function and evolution of genomes

Question 2

what is transcriptomics

Answer 2

study of global RNA expression

Question 3

what is genotyping

Answer 3

measurement of DNA diversity through polymorphisms and mutations

Question 4

what is epigenomics

Answer 4

epigenetic modification of the DNA and its effect in gene expression

Question 5

what is comparative genomics

Answer 5

study of differences and relationships between the genome sequence and function across different strains or species

Question 6

what is synteny

Answer 6

the conservation of blocks of order within two sets of chromosomes that are being compared with each other

Question 7

what is average nucleotide identity

Answer 7

a category of computational analysis that measures the nucleotide level genomic similarity between two genomes

Question 8

how is ANI usually represented

Answer 8

as a heatmap

Question 9

what are protein clusters

Answer 9

groups of similar proteins that most likely share the same or similar function

Question 10

do protein clusters consists of orthologs or paralogs

Answer 10

orthologs

Question 11

what is the pan genome

Answer 11

represents the entire set of genes found in all strains within a clade

Question 12

what are the three sections in a pan genome

Answer 12

core, shell and cloud

Question 13

what is the core genome

Answer 13

contains genes present in all individuals

Question 14

what is the shell genome

Answer 14

contains genes present in two or more strains

Question 15

what is the cloud genome

Answer 15

contains genes only found in single strain aka accessory aka dispensable aka truly unique genes

Question 16

what can the core genome be divided into

Answer 16

hard core and soft core

Question 17

what is hard core genome

Answer 17

at least one copy of the family shared by every genome

Question 18

what is soft core genome

Answer 18

families distributed above a certain threshold

Question 19

what is the model used to fit a pan genome function

Answer 19

Heaps law

Question 20

examples of cloud genes

Answer 20

ecological adaptation, antibiotic resistance, HGT

Question 21

examples of cloud genes

Answer 21

ecological adaptation, antibiotic resistance, HGT

Question 22

what are the ANI cut off levels for species, genus and family

Answer 22

species - 95%
genus - 74%
family - 70%

Question 23

what is pan genome analysis software

Answer 23

roary using sequence alignment MAFFT and analysed by scoary

Question 24

what is a microbiome

Answer 24

community of microorganisms living together

Question 25

what are the two main approaches in microbiome profiling

Answer 25

16S rRNA sequencing and Deep sequencing

Question 26

what is relative species abundance

Answer 26

measure of how common or rare each species is relatively to other species in a defined community

Question 27

what is relative species abundance useful for

Answer 27

determine the dominant microbial taxa, not to be compared between samples

Question 28

what is absolute species abundance

Answer 28

the absolute quantification of an organism in a defined community, requires a known internal standard

Question 29

what is alpha diversity

Answer 29

the mean diversity of species in different sites or habitats

Question 30

what is beta diversity

Answer 30

ratio between regional and local species diversity

Question 31

what is an operational taxonomic unit

Answer 31

unique biological sequence organised in tables containing number of reads

Question 32

what does 16S rRNA sequencing detect

Answer 32

who is there- species composition

Question 33

what is the pipeline for performing 16S rRNA sequencing

Answer 33

QIIME

Question 34

what is whole shotgun sequencing

Answer 34

sample all genes in all organisms present in a sample