Memorize Flashcards
Genetic or physical - RFLP?
Genetic
Genetic or physical - SNPs
genetic
Genetic or physical - SSLP
Genetic
Genetic or physical - Restriction site mapping
physical
Genetic or physical - FISH
Physcial
Genetic or physical - STS
physical
RFLP?
Restriciton fragement length polymorphism
SSLP?
simple sequence length polymorphism
types of SSLPs?
minisatallites + microsatellites
minisatellites
a) length of repeats
b) distribution in the genome
c) total length
a) 25bp
b) telomeres
c) several kbps
Microsatellites
a) length of repeats
b) distribution within genome
c) total length
a) 6-13bp
b) evenly spread throughout genome
c) less than 300bp
Match the following
1. Minisatalliets
2. microsatellites
a) variable number of tandem repeats
b) simple tandem repeats
1a, 2b
SNP?
single nucleotide polymorphism
Haplotype
a short stretch of SNP that are closet together and tend to be inherited together
Number of base pairs shown
a) high-resolution
b) low-resolution
a) 1-100 kbp
b) several Mbps
Physical mapping
a) actual or relative position
b) does it use independent recombination?
c) does it use polymorphism
a) actual
b) no
c) no
Genetic mapping
a) actual or relative position
b) does it use independent recombination?
c) does it use polymorphism
a) relative
b) yes
c) yes
FISH
fluorescent in situ hybridization probe
STS
sequence tag sites
Distance btw each physical marker
1 marker per 100kb
how is genetic maping measured?
cM
how many cM per 1Mbp
1
summarize genetic maps
Genetic maps are dependent on recombination
frequency which allows the ordering of markers
relative to one another. Requires polymorphisms
summarize physcial maps
Physical maps show the physical distance between
markers, can be of low or high resolution. Requires
non-polymorphic markers. Independent of
recombination
what is the general-sized fragments used in the shotgun method
1.6 - 2 kb
what is the length of each read generated by the shotgun method?
800-1000bp
Which genome does the shotgun method tend to read
H. influenza
match the following to either low or high resolution
a) giemsa staining
b) FISH
c) radiation hybrid maps
d) STS/SSLPs
e) restriction site mapping
f) nucleotide sequence
a) low
b) low
c) modertate to high
d) moderate-high
e) high
f) high
Shotgun method
a) benefits
b) limits
a) good for smaller genomes without significant repeats, faster and cheaper, and can sequence unknown sequences
b) not good for larger genomes with significant repeats
contig method
a) benefits
b) limits
a) can handle repetitive sequences and larger genomes
b) slower and more expensive and needs to use a physical map for reference
what are 3 modifications of open reading frame scanning
- codon bias
- exon-intron boundaries
- upstream regulatory sequences
ORF
open reading frame
methods to identify genes (name at least 4)
- look for ORFs
- intron-exon boundaries to look for consensus splice acceptor and splice donor sites
- Condon bias
- CpG islands
- locating fxnal RNAs (unique seq that don’t code for genes)
- homology search (comparing known genes)
- conservation of synteny
conservation of synteny
preservation fo gene order on a chromosome
how many genes in human genome
20000
human genome
a) gene density
b) introns per gene
c) amount of the genome that is taken up by genome-wide repeats
a) 11
b) 9
c) 44%
Fill in the blank
1. Size of the organism is ________ to the size of its genome or the number of genes, especially in eukaryotes. (correlated or not correlated)
b) The complexity of an organism is _______ to the size of its
genome (correlated or not correlated)
c) The size of the genome ______ to the density of the genes. (correlated or not correlated)
d) The more dense the genes, the _______ the genome. (larger or smaller)
e) Complexity _____ related to the amount of non-protein coding
regions (is or is not)
a) not correlated
b) not correlated
c) correlated
d) smaller
e) is
% of genome: Genes and gene-related sequences
38%
% of genome: exons
1.5%
% of genome: related sequences
36.5%
% of genome: intergenic DNA
62%
% of genome: genome-wide repeats
44%
% of genome: other intergenic regions
18%
4 types of genome-wide repeats
- LINES
- SINEs
- LTR elements
- DNA transposons
LTR
long terminal repeats
SINE
short interspersed nuclear elements
LINEs
long interspersed nuclear elemnets
GWR
genome wide repeats
types of DNA transposons
- conservative
- replicative
SINE
a) family
b) approx number of copies
c) fraction of genome
d) length
a) Alu
b) 1.2 million
c) 10.7%
d) 100-400bp
LINES
a) family
b) approx number of copies
c) fraction of genom
d) full length
a) LINE-1
b) 1 million
c) 21%
d) 900bp
LTR retroelements
a) family
b) approx number of copies
c) fraction of genome
d) length
a) ERV
b) 240000
c) 4.7%
d) 6-11kb
DNA transposons
a) family
b) approx number of copies
c) fraction of genome
d) average length
a) MER-1
b)350000
c) 2.8%
d) 100-10000bp
GC content
a) LINES
b) SINES
a) GC poor
b) GC rich
total number of CpG islands by GC content
28890 islands
correlation btw GC content and;
a) CpG island density
b) gene-density
c) intron length
d) exon length
e) Giemsa staining (dark or light)
f) LINES (poor or rich)
g) SINES (poor or rich)
a) positive
b) positive
c) negative
d) no relationship
e) light
f) poor
g) rich
match term to the definition
1. homologue
2. orthologue
3. paralogue
a) genes in different species that evolved from a common ancestral gene by speciation
b) A gene related to a second gene by descent from a common
ancestral DNA sequence
c) genes related by duplication within a genome
1b,2a,3c
Match the following with genoem structure (GS), coding regions (CR) or non-gene regions (NGR)
a) GWR
b) transposon selectivity
c) exon-intron boundaries
d) conserved domain
e) number of genes
f) gene density
g) synteny
h) protein sequence
I) conserved fxn
GS: e,f, g
CR: c, d, h, i
NGR: a,b
pufferfish
a) number of genes
b) transposons
c) size relative to a human genome
a) 27918
b) 4000
c) 1/10th
3 - 2nd generation sequencing tech
- pyrosequencing
- sequencing by ligation (Solid)
- sequencing by synthesis
2 - 3rd generation sequencing technologies
- single molecule sequencing
- nanopore sequencing
2 types of PCR
- emulsion
- bridge
name fxn of each enzyme
a) sulfurylase
b) luciferase
c) apyrase
a) converts PPi into ATP
b) converts ATP into light
c) washes the NTPs away
Pyrosequencing
a) read lengths
b) number of b/run
c) ____ error rate (high/low)
a) 200-300bp
b) 80-150Mb/run
c) high
SoLid
a) read lengths
b) number of b/run
c) ____ error rate (high/low)
d) __ possible probes
a) 35b
b) 1-3Gb/run
c) low
d) 16
Illumina/Solexa
a) read lengths
b) number of Mb/run
c) ____ error rate (high/low)
a) 30-40b
b) 1Gb/run
c) high
SMRT
single molecule real time
Does 3rd generation sequecning need amplificiation of DNA?
no
Microarray
a) advantages
b) disadvantages
a) low cost
b) analysis pre-defined sequences, high variation for low expressed genes
RNA-seq
a) advantages
b) disadvantages
a) not reliant on prev sequence info, can detect alternative splicing, can define paralogous genes
b) high cost, high data,
