Genomics Flashcards
what is genomics
study structure, function and evolution of genomes
what is transcriptomics
study of global RNA expression
what is genotyping
measurement of DNA diversity through polymorphisms and mutations
what is epigenomics
epigenetic modification of the DNA and its effect in gene expression
what is comparative genomics
study of differences and relationships between the genome sequence and function across different strains or species
what is synteny
the conservation of blocks of order within two sets of chromosomes that are being compared with each other
what is average nucleotide identity
a category of computational analysis that measures the nucleotide level genomic similarity between two genomes
how is ANI usually represented
as a heatmap
what are protein clusters
groups of similar proteins that most likely share the same or similar function
do protein clusters consists of orthologs or paralogs
orthologs
what is the pan genome
represents the entire set of genes found in all strains within a clade
what are the three sections in a pan genome
core, shell and cloud
what is the core genome
contains genes present in all individuals
what is the shell genome
contains genes present in two or more strains
what is the cloud genome
contains genes only found in single strain aka accessory aka dispensable aka truly unique genes
what can the core genome be divided into
hard core and soft core
what is hard core genome
at least one copy of the family shared by every genome
what is soft core genome
families distributed above a certain threshold
what is the model used to fit a pan genome function
Heaps law
examples of cloud genes
ecological adaptation, antibiotic resistance, HGT
examples of cloud genes
ecological adaptation, antibiotic resistance, HGT
what are the ANI cut off levels for species, genus and family
species - 95%
genus - 74%
family - 70%
what is pan genome analysis software
roary using sequence alignment MAFFT and analysed by scoary
what is a microbiome
community of microorganisms living together
what are the two main approaches in microbiome profiling
16S rRNA sequencing and Deep sequencing
what is relative species abundance
measure of how common or rare each species is relatively to other species in a defined community
what is relative species abundance useful for
determine the dominant microbial taxa, not to be compared between samples
what is absolute species abundance
the absolute quantification of an organism in a defined community, requires a known internal standard
what is alpha diversity
the mean diversity of species in different sites or habitats
what is beta diversity
ratio between regional and local species diversity
what is an operational taxonomic unit
unique biological sequence organised in tables containing number of reads
what does 16S rRNA sequencing detect
who is there- species composition
what is the pipeline for performing 16S rRNA sequencing
QIIME
what is whole shotgun sequencing
sample all genes in all organisms present in a sample
