12.1 Flashcards
what is shotgun sequencing?
genomic DNA is sheared into short sequences and sequenced by next gen
assembler software looks for overlaps to assemble them into contigs
what is the issue with shotgun sequencing?
has issues with repetitive sequences (nanopore helps with this)
what are the advantages of long reads?
help with assembly and alignment of short reads
what is read or sequencing depth?
number of times a base is represented within all the reads from a sequencing run
gives greater confidence
what is a good sequencing depth?
> 100 for a new genome
what is the math of sequencing depth?
average number of times one spot is sequenced
what is genome assembly?
next gen and 3rd gen sequencing of all chromosomes
what is transcriptomics?
next gen sequencing of all mRNA transcripts
what is species identification?
sanger sequencing of one gene
COI (mtDNA) for animals
16srDNA for microbes
nucleur rDNA for fungi
cpDNA for plants
what is evolutionary relationships anaylsis?
sanger and next gen sequencing of whole genome
what is microbial ecology?
next gen sequencing of 16srDNA (for microbes)
what is environmental DNA?
next gen sequencing of mtDNA
why is mtDNA good for sequencing?
we have lots of copies of it and evolves at just the right rate
who invented minisatellite DNA?
alec jeffries
what are minisatellites?
small (10-100 bp sequences) that are repeated many times (up to 1000) in tandem arrays
why are mini satellites important?
they have a ton of allelic variation due to mutations (slippage errors and unequal cross-over) that make them different in every person)
what are microsatellites?
smaller minisatellites that can be amplified using pcr instead of southern blotting
what are the other names for microsatellites?
STRs and SSRs
how does microsatelite genotyping happen?
fluorescent primers are used to amplify
products are separated by electrophoresis
genotypes are identified by size of products
what is multiplex analysis?
multiple microsatellites amplified at the same time using primers with different colours
how do microsatellites cause genetic disorders?
involve trinucleotide repeats within genes
have versions with too many repeats
what are examples of microsatellite genetics disorders?
huntington’s, myotyonic dystrophy, fragile X syndrome
what is RFLP analysis?
restriction fragment length polymorphism analysis to detect them in gel electrophoresis
what are RFLPs?
mutations that either create or destroy restriction endonuclease sites
what are RFLPs caused by normally?
SNPs - single nucleotide polymorphisms
what are SNPs caused by?
usually a single base mutation (most common genetic variation)
what is a haplotype?
arbitrarily long stretch of DNA characterized by particular alleles at the SNP positions in the sequence
what causes haplotypes?
SNPs that are close together and get inherited together
what are SNP chips?
microarrays - use dna hybridization-based assay to determine genotypes at known SNPs
what is GWAS?
genome wide association studies
what is the point of GWAS?
looking for genetic links to diseases by looking for SNPs that are correlated with presence of disease
