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Genomics > Vocabulary Words For Exam 1 > Flashcards

Vocabulary Words For Exam 1 Flashcards

1
Q

Heteroplasmy

A

The situation in which two or more mtDNA exists within the same cell

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2
Q

Histones

A

any of a group of basic proteins found in chromatin

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3
Q

Heterochromatin

A

chromosome material (compacted) in which the activity of the genes is modified or suppressed

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4
Q

Euchromatin

A

Chromosome material that is active

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5
Q

Nucleosome

A

the fundamental repeating unit of chromatin

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6
Q

Constitutive heterochromatin

A

the DNA sections of the chromosomes that remain constant throughout the cell cycle

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7
Q

Centromeres

A

the region of a chromosome to which the microtubules of the spindle attach during cell division

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8
Q

Telomeres

A

a compound structure at the end of a chromosome

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9
Q

Segmental duplications

A

blocks of DNA that typically share more than 90% sequence identity and occur at more than one site within the genome

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10
Q

Phosphodiester bonds

A

a chemical bond of the kind joining successive sugar molecules in a polynucleotide

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11
Q

Polarity

A

Direction

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12
Q

DNA polymerase

A

a type of enzyme that is responsible for forming new copies of DNA, in the form of nucleic acid molecules

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13
Q

Semiconservative

A

during DNA replication, the two strands of the nucleotides separate and each daughter strand has half of the original DNA

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14
Q

Base Pair

A

bp 1

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15
Q

Kilobase

A

Kb 1,000 (1,000 bp)

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16
Q

Megabase

A

Mb (1,000,000) (1000 Kb)

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17
Q

Gigabase

A

Gb 1,000,000,000 (1000Mb)

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18
Q

Terabase

A

Tb 1,000,000,000,000 (1000 Gb)

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19
Q

Petabase

A

Pb 1,000,000,000,000,000 (1000 Tb)

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20
Q

Denaturation

A

the unfolding or breaking up of a protein, modifying its standard three-dimensional structure

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21
Q

Annealing

A

process of joining of single-stranded DNA or RNA with hydrogen bonds to form a double-stranded polynucleotide

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22
Q

Extension

A

using the loosened nucleotides of each base to grow the complementary DNA strand

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23
Q

PCR

A

Polymerase Chain Reaction
a lab technique for rapidly producing millions to billions of copies of a specific segment of DNA

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24
Q

Regulatory Promotor

A

Upstream of core promoter
the binding site for the transcription apparatus

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25
Q

Transcription factors

A

proteins that help turn specific genes ‘on’ or ‘off’ by binding to nearby DNA

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26
Q

Enhancers

A

distal locations can also enhance transcription

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27
Q

Gene

A

fundamental unit of heredity

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28
Q

TSS

A

transcription start site

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29
Q

5’ cap

A

put on the 5’ side used to protect the end

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30
Q

3’ poly (A) Tail

A

line of As put on the 3’ end to protect that end

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31
Q

Degenerate

A

repetative

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32
Q

Synonymous

A

change in DNA seq does not change AA

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33
Q

Wobble

A

the 3rd base of the codon can vary

34
Q

Non-synonymous

A

change in DNA seq changes AA

35
Q

Nonsense

A

change in DNA is a stop codonA

36
Q

AUG

A

start codon
methionine

37
Q

Reading frame

A

code is read in threes

38
Q

Template

A

DNA used as input to create a library

39
Q

Library

A

temple DNA that has undergone all the manipulations to enable it to be sequenced

40
Q

Adapters

A

specific sequence added to the 5’ and 3’ ends of template DNA that are complementary to the oligos on the flow cell

41
Q

Indexes/barcodes/tags

A

A unique DNA sequence ligated to fragments within a sequencing library for downstream in silico sorting and identification

42
Q

Flow cell

A

a glass slide with one, two, four, or eight physically separated lanes. Each lane is coated with a lawn (nano-well) of surface bound, adapter-complimentary oligos

43
Q

Bridge amplification

A

the process where a single molecule is amplified to form a cluster

44
Q

Cluster

A

clonal grouping of template DNA bound to the surface of a flow cell

45
Q

Fluor

A

chemical structure that emits light at a certain wavelength when excited by laser

46
Q

SBS

A

sequencing by synthesis
one nucleotide is added at a time

47
Q

biological nanopores

A

alpha-hemolysin is a heptameric protein pore with an inner diameter of a few nm, 100,000 times smaller than a human hair

48
Q

Homopolymers

A

same sequence of multiple nucleotides
can be an error point because it does not change the chemical structure and the machine is not sure how many to read

49
Q

ZMWs

A

zero-mode wave guides
nano-wells used in PacBio

50
Q

SMRT sequencing

A

single molecule real time

51
Q

indels

A

an insertion or deletion of bases in the genome of an organism

52
Q

FASTA

A

standard file format used when quality is not needed
presents only the sequence itself

53
Q

FASTQ

A

standard file format used when quality is needed
contains the sequence and the estimated base quality

54
Q

QPhred

A

-10log10 P(error)

55
Q

Alignment

A

a set of columns, each containing a set of bases that are all related to each other by some alignment relation

56
Q

Smith-Waterman

A

one of two main algorithms
find the optimal local alignment
good for Sanger but too slow for high throughput

57
Q

Burrow-Wheeler Transform

A

creates suffix array of smaller k-mers
match the seed of the read to the reference
extend seed to full alignment
BWA (WGS) and STAR (RNA)
most used aligner

58
Q

Minimap

A

long reads alignment algorithm

59
Q

optimal local alignment

A

an alignment giving the highest score

60
Q

variants

A

differences between our sample and the reference

61
Q

SNPs

A

single nucleotide polymorphisms

62
Q

SAM

A

sequence alignment map
11 mandatory fields

63
Q

BAM

A

binary (compressed) version of SAM
8 mandatory fields

64
Q

Variant call format

A

a standard text file used in bioinformatics for storing gene sequence variations

65
Q

BCF

A

binary of VCF

66
Q

BaseQualityScoreRecalibration (BQSR)

A

uses a set of known variant positions and considers all other variants from sequence data as errors
builds a model based on several parameters

67
Q

Samtools mpileup

A

variant caller-not used much anymore
provides a summary of the coverage of mapped reads on a reference sequence at a single base pair resolution

68
Q

GATK HaplotypeCaller

A

Most used variant caller
call potential variant sites per sample and save results in GVCF format

69
Q

Single sample variant calling

A

only shows one sample

70
Q

Joint variant calling

A

shows multiple samples
is preferred

71
Q

Hard filtering

A

based on multiple metrics and filters variants

72
Q

sensitivity

A

true positive rate
measures the proportion of positives that are correctly identified
(proportion of those who have some condition who are correctly identified as having the condition)

73
Q

Specificity

A

true negative rate
measures the proportion of negatives that are correctly identified
(proportion of those who do not have the condition and are correctly identified as not having the condition)

74
Q

VariantQualityScoreRecalibration

A

similar to BQSR but for variants

75
Q

truth set

A

a list of variants that is used to evaluate the quality of a variant callset

76
Q

Tranches

A

slices of variants, ranked by VQSLOD

77
Q

90 tranche

A

few variants but also few false positives
miss true positives but don’t have as many false positives

78
Q

100 tranche

A

many variants but also many false positives
capture true positives but have many false positives

79
Q

High tranche

A

if you want more variants and are willing to accept false positives

80
Q

Middle Tranche

A

if you want to remove most false positives but are also willing to remove some true variants

81
Q

low tranche

A

if you only want highly accurate true variants with few false positives and willing to miss perhaps many true positives

Genomics (11 decks)

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