Genomics Flashcards
What is genomics, what are the areas of inquiry
the study of whole genomes in their entirety
-structural, functional, and comparative genomics
what is bioinformatics used for and algorithms
-organize, share and analyze data related to: gene structure, sequence and expression, protein structure and function
T/F both subunits of insulin are needed to unite and make insulin
TRUE
T/F transgenic coho salmon express the growth hormone gene only in spring and summer
TRUE
T/F next generation sequencing uses in vivo cloning and amplification
FALSE
T/F next generation sequencing uses cyclic flowcell sequencing
TRUE
what is the benefit of whole genome sequencing
all DNA fragments can be sequenced without the need to insert DNA fragments into vectors and cloning them in host cells
how do restriction enzymes help WGS and assembly?
examples and how many contigs they give?
they create a series of overlapping fragments
-EcoRI: contigs 1, 2-4
-BamHI:1-2, 3, 4
what is a contig?
process of alignment?
contigs: overlapping fragments that collectively form one continuous DNA molecule within the chromosome
Alignment: alignment of contigs allows for a completely sequenced chromosome
main problem of repetative DNA?
how does pair-end sequencing fix it?
-since repeats are identical they can not be assigned to a unique genomic location
-it uses repeats in assembling scaffold to contain the repetitive clone
paired end sequencing correlation of insert size and sequence coverage
Insert Size Coverage
2-3 8X
6-8 2x
20-30 0.5X
process of de novo assembly
overlapping DNA sequences into entire chromosomes
T/F PacBio SMRT sequencing uses nanopore and electrical signature for each nucleotide
FALSE. oxford nanopore does
what is used to resequence human genomes
reference based genome assembly
how are SNPs, INDLs, and CNVs part of WGS
SNP: single nucleotide polymorphism
INDL: large scale structural variations
CNV: copy number variant, repeat of a section of the genome greater than 1 kb
ortholog v paralog
orthologs: genes from different species thought to have descended from the same ancestor(same function)
paralogs: same species but originate from duplication(different function)
most important part of building a genome sequence
annotation
what percent of the genome codes for proteins?
how many genes does it make?
<2% codes for proteins
20,000 genes
alternative splicing leads to _____ number of genes than the number of predicted genes
greater
T/F WES(whole genome sequencing) fails to identify gene regulatory regions that influence gene expression
TRUE
2 transcriptomic methods discussed in class
qualitative: what is vs isn’t expressed
quantitative: measures levels of expression
proteomic uses _____ for separating hundreds of thousands of _____ with high resolution
two dimensional gel electrophoresis(2DGE), protein
mass spectrometry uses what to measure ratio of different ions in sample
mass-to-charge(m/z)
what are homologous genes in relation to genomics
evolutionarily related genes
