bioinformatics midterm

Genotype

Complete genetic material of an organism

Phenotype

Observable characteristics of an individual

Epigenetics

Non heritable changes to the genome

Allele

A variant of a DNA sequence at a specific locus

Econ

Part of the gene that stays in the final mature mRNA

Intron

Non-coding sequence that is cut out before the molecule becomes a mature mRNA

Domains

Distinct compact regions of proteins that can fold independently and have specific functions

Modular proteins

Proteins composed of multiple domains

Transcriptome

All the RNA being transcribed

Proteome

All the proteins being translated

RNA NCBI databases

Gene, GEO profiles, UniGene

Homology

Trait inherited through a common ancestor

Homolog

gene, protein or sequence that shares a common ancestor with another sequence

Ortholog

Gene in a different species evolved from a common ancestor separated by a speciation event

Paralog

A gene sharing a common ancestor that diverged through a duplication event

Pairwise alignment

Lining up two sequences to identify regions of similarity

Phylogeny

A diagram visualizing hypothetical evolutionary pathways and common ancestors

LINEs

A group of autonomous non-LTR retrotranscriptons comprising a large portion of eukaryotic genomes

Genome assembly

The process of taking millions of “reads” and pricing them together to construct the original chromosome or genome

Genome assembly patch

A localized scaffold sequence released to update an existing reference genome

Karyotype

The complete set of chromosomes of an organism

Fluorescence in situ hybridization

A method using fluorescently labeled single stranded probes to detect specific complimentary sequences on chromosomes

BAC map

Genome wide map built of overlapping cloned segments of genomic dna

Locus

A specific fixed position on a chromosome where a particular gene or marker is located

Scaffold

A genomic sequence made by linking two or more non continuous contiguous into an ordered structure

Contig

A continuous sequence of dna formed by aligning and joining dna fragments without gaps

SNPs

A variation in dna where a single nucleotide differs

cDNA

A synthetic form of dna made from a RNA template

Open Reading frame

A continuous stretch of sequence that begins with a start codon to a stop codon

Splice junction

The contact point where introns are removed and exons are joined together

TF binding sites

The sequence where transcription factor proteins bind to activate or repress expression

Haplotype

Group of alleles or genetic variants that are inherited together from a single parent due to proximity on the chromosome

Haplotype block

A continuous region of chromosome where recombination is rare causing inheritance as a single unit

Tag SNP

A representative SNP chosen in a genomic region that serves as a proxy for a group of neighboring SNPs

Copy number variation (CNV)

A structural genomic variant where the number of copies of a DNA segment differs from the standerd refrance

Identity

The extent to which two sequences are invariant

Conservation

Changes at a specific position of a sequence that preserve the physico-chemical properties of the original

Similarity

The extent to which sequences are related. Based on Identity + Conservation

E value

The number of different allignments expected to occur by chance, that have a score of S or better given the size of the data base

Score

The sum of match, mismatch, gap creation, and gap extension scores in a BLAST search

Point accepted mutation (PAM) matrices

Matrices based on global alignments of closely related proteins. to represent an evolutionary distance of 1 accepted point mutation per 100

BLOSUM

Matrices based on observed alignments

Log odds scoring matrix

Assigns scores based on how likely AA substitution is. Is part of PAM

Nodes

Connect two or more branches and represent most common ancestor

Tip (aka: leaf)

Represent genes or taxa on the tree

Cladogram

Shows topology but not distance and no information on genetic distance

Phylogram

Shows topology and distance. Branches proportional to genetic distance

scaled vs unscaled

Tips unaligned and proportional to substitutions vs tips aligned branches not proportional to distance, nodes represent time

Bifurcating

All nodes resolved and all taxa are known how related

Multifurcating

Some nodes unresolved, not all relationships of taxa known

Rooted tree

Identify Basel ancestor of all tips

Outgroup

A reference taxa more distantly related to the study group than other taxa

Newick format

tips grouped by parentheses, nodes identified with comas, length of branch noted with colon

Clade

A branch on a tree representing a group consisting of a common ancestor and it’s descendants

Monophyletic

Includes all descendent taxa of a single common ancestor

Paraphyletic

Clade that included the common ancestor but is missing one or more of the descendent taxa

Polyphyletic

Clade with taxa that do not share an immediate common ancestor

Synapomorphys

Shared derived characteristics to infer ancestry due to similarities

Homoplasies

Similarity’s as a result of convergent evolution resulting in independent derivatives similar characteristics

Species tree

Speciation when reproductively isolated. Internal nodes represent speciation events

Gene tree

Genes can evolve before or after speciation event and can be effected by unique evolutionary processes

Hamming distance

The degree of divergence in substitution models

Maximum parsimony

Finds the one tree with the fewest number of changes given the data, assigns a cost to each tree and finds the lowest cost

Maximum likelihood

Find the one tree with the single highest likelihood

Bayesian inference

Finds the one tree with the highest probability distribution

Bootstrap analysis

Subsample sequence and rebuild lots of trees then find the consensus tree

Jackknife analysis

Remove while gene or species and rebuild tree

Proportion of invariable sites

Extent of static unchanging sites in a dataset

Gamma distribution

Gamma distributed rate variation among sites

Disparity index

The observed difference in evolutionary patterns for a pair of sequences based on composition

Synonymous substitutions

Do not change the amino acid sequence, usually neutral

Non symonomus

Change the amino acid sequence and are more likely to change protein function

Positive selection

dN/dS = >1

Purifying selection

dN/dS = <1

Sequence evolutionary rate

The fraction of sites that undergo a change in a designated time frame