Bioinformatics Midterm

Natural selection

Adaptations where selective pressure only allows species with better fitness to survive

Genotype

Genetic variants in the genome

Phenotype

Phenotype is the trait that results from the organism’s life history, environment, epigenetics, and genotype

Life history

Sum total of past and present environments

Epigenetic factors

Non-heritable changes to DNA

Allele

Alternate form of a gene

Population

Group of same species that lives in the same area

Mutations

Heritable change to the genome

Recombination

Process of chromosomes receiving a unique set of genetic information during meiosis. Close chromosomes are more likely to be inherited as a set and far apart chromosomes are more likely to be inherited independently

Gene duplication

Extra copies of the gene are created

Gene loss

Copy of a gene is removed

Gene flow

Transfer of genetic material between populations

Microevolution

The evolution that occurs within a population over a relatively short time scale, often involving small genetic changes that can lead to variations in traits

Macroevolution

The evolution that occurs over long periods of time and typically results in the formation of new species

Central Dogma

The process of information going from the genome to the transcriptome and finally to the proteome

Exon

Part of DNA that is included in the mature mRNA

Intron

Part of DNA that is removed from the mature mRNA

Codons

A set of three nucleic acids that codes for a particular animo acid

Side chain

The part of the amino acid that determines the folding, bond formation, and effects interactions

Folding pattern

The way a sequence of amino acids arranges itself within 3D space many factors contribute to this process

Primary structure

The sequence of amino acids in a peptide

Secondary structure

Formation of peptide chains into higher structures such as alpha helixes and beta sheets

Tertiary structure

Recurring patterns of interactions between helices and sheets

Supersecondary structure

A compact arrangement of secondary structure motifs that is smaller than a domain

Domains

compact units within
The folding pattern of a single chain that appears
independently stable, each has specific function(s)

Modular proteins

Contains multiple copies of the same domain

Databases

Organized sets of data that are typically sorted by data type (ex a DNA sequence database)

Homologous

Feature is due to a related structure in a common ancestor

Common ancestor

The most recent ancestors that is related to two species that diverged from that common ancestor

Similarity

The extent to which nucleotide or protein sequences are related. Based on identity and conservation

Homolog

A sequence that is similar due to shared common ancestry

Ortholog

Homologous sequences in different species that arose from a common ancestral gene during speciation. May or may not be responsible for a similar function

Paralog

Homologous sequences within a single species that arose by gene duplication

Convergent evolution

Independent origin of trait or phenotype

Pairwise alignment

The process of lining up two sequences in order to achieve maximal levels of identity for the purpose of assessing the degree of similarity

Phylogeny

Inference of evolutionary relationships reconstructed as a tree diagram

LINES

Repetitive element consisting of long interspersed nuclear elements

SINES

Repetitive element consisting of short interspersed nuclear elements

Genome assembly

Sequence of an entire genome ordered as the continuous DNA molecules that make up each chromosome

Scaffold

A portion of the genome that consists of gaps and contigs

Contig

A continuous sequence

NGS

Next generation sequencing is a field of bioinformatics that aims to expand the methods for rapidly sequencing DNA and RNA

Illumina

Newer method of sequencing that shreds the entire genome into 400-600 base pair fragments. This method can read 600 million of these fragments at once

Nanopore

A small portable device that is capable of rapidly sequencing entire genomes

Karyotype

The complete set of chromosomes for an organism

G-banding

Giemsa stain that stains the A-T rich regions a darker color than the rest of the chromosome. Each chromosome has a unique G-banding pattern that is used to number chromosome regions

Linkage map

Gives a visual representation for the distance that genes are apart on a chromosome. This determines the likelihood of them being inherited together

Recombination frequency

Used to group and order genes, 1% recombination is equal to 1 centiMorgan

FISH

Fluorescent in situ hybridization which is used to verify that genome assembly is correct by fluorescently labeling DNA to be viewed under a microscope

BAC map

A method to create scaffolds by using chromosome sections that are inserted into plasmids and replicated in bacteria. The bacterial artificial chromosomes are ordered into a map using genetic markers

Marker

A known location on a chromosome that is useful for identification

Locus

A specific location on a chromosome

Human genome hg38

The current version of the human genome which was created in December 2013

UCSC Genome Browser

An interactive collection of a variety of genome sequences of many types of species

Gene model

The most basic annotation defining the start and stop of a sequence that is transcribed to RNA and preforms a function

Open reading frame

Sequence of DNA that can be translated into a protein and contains a start and stop codon

Promotor

A DNA site upstream from the protein coding region that indicates where transcription proteins should begin 

Splice junction

The process of removing introns from RNA

5’UTR

Is upstream of the initiation codon

3’UTR

Is downstream of the initiation codon

TF binding sites

The location on DNA where the transcription factor binds to begin transcription

cDNA

Complementary DNA that is used to measure the amount of expression of different genes

RNAseq

A technique that determines what RNA is present in a cell and how much of it. Gives a snapshot of the transcriptome of the cell

GWAS

Genome-wide association studies looks at many individuals with genetic variants to determine if that variant is associated with a specific trait

SNP

Single nucleotide polymorphisms are variations at a single position in the DNA sequence

Tag SNP

A region in the genome that has high linkage disequilibrium and represents a groups of SNPs called a haplotype

Haplotype

A group of alleles that are inherited together from a single parent

Haplotype block

Region of an organism’s genome where there is little evidence of genetic recombination

International HapMap Project

Goal was to develop a haplotype map for the human genome

1,000 Genomes Project

The replacement for the International HapMap Project

Aliphatic

Compounds that consist entirely of carbon and hydrogen in a straight line

Aromatic

Containing at least one aromatic ring with alternating double bonds

Polar/nonpolar

Specifies whether or not the compound contains a dipole

Homology

Trait or sequence inherited by a common ancestor

Identity

The extent to which two sequences are invariant

Conservation

Changes at a specific position of an amino acid or sequence that preserve the physio-chemical properties of the original residue

Score

Determines how well the sequences align

Identities

Gives the number of residues within the sequence that are an exact match

Positives

Gives the number of residues within the sequence that are similar

Log-odds score

Score aligned positions based on the likelihood of a mutation occurring

Substitution Matrix

Contains values proportional to the probability that amino acid i mutates into amino acid j for all pairs of amino acids. Constructed by assembling a large and diverse sample of pairwise alignments

PAM

Point accepted mutation is based on global alignments of closely related proteins

BLOSUM

Blocks substitution matrix is based on observed alignments that are not extrapolated

BLAST

Allows rapid sequence comparison of a query sequence against a database

E-value

The expect value is the number of different alignments expected to occur by chance that have a score of S or better given the database (lower = a better match)

NR database

The non-redundant nucleotide database contains all the nucleotide sequences available on NCBI

RefSeq database

A publicly available database of available nucleotide sequences 

DELTA-BLAST

Domain enhanced lookup time accelerated works best for more distantly related proteins

Conserved domain database

A database containing annotated protein sequences

Homologous sites

Refer to features that share a common evolutionary origin

Ancestral sites

Refer to the common ancestors from which homologous sites evolved

Structural sites

Features that have a similar function but do not have a common ancestor

Disulfide bridges

Occur between two cysteine residues. The bond forms between the two sulfur atoms

Transmembrane regions

The nonpolar region of the peptide chain that interacts with the hydrophobic membrane core

Progressive alignment

First aligns the most similar sequences then additional sequences are progressively aligned to the existing alignment

Needleman & Wunsch dynamic programming

Program gives a score to every possible alignment in order to find the best alignment

Guide tree

Tree calculated from the distance matrix

Gaps

Missing sequences

CLUSTAL

Uses progressive alignment, ideal for smaller alignments

MUSCLE

Uses progressive alignment, ideal for larger alignments, more accurate than CLUSTAL