25
Dec
2009
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Glossary

A B C D E F G H I J K L M N O P Q R S T U V W X Y Z

P

P
Proline.
palindromic sequence
A DNA or RNA sequence that reads the same on the complementary strand (e.g., AATGCATT). A DNA or RNA sequence that shows symmetry about a central axis point.
PAML
Phylogenetic Analysis using Maximum Likelihood.
parallel substitutions
The independent occurrence of the same mutation at the same nucleotide site in two or more lineages.
paralogy
Sequence similarity between the descendants of a duplicated ancestral gene.
pararetrovirus
A virus that contains a gene for reverse transcriptase but cannot insert itself into the host chromosome.
parsimony
Literally, the use of a minimum number of means to achieve an end. (see maximum parsimony)
pattern of substitution (substitution scheme)
The relative frequency with which a nucleotide or an amino acid changes into another during evolution.
PAUP*
Phylogenetic Analysis Using Parsimony, *and other methods (pronounced pop star).
PCR (polymerase chain reaction)
A technique for amplifying DNA sequences in vitro by separating the DNA into two strands and incubating it with oligonucleotide primers and DNA polymerase.
phase-0 intron
An intron that lies between two codons.
phase-1 intron
An intron that lies between the first and second nucleotides of a codon.
phase-2 intron
An intron that lies between the second and third nucleotides of a codon.
phenogram
A graphic representation that portrays or attempts to portray the taxonomic relationships among a number of individuals, species, or higher taxa on the basis of overall similarities between them.
phenotype
The observable characteristics of a genetically controlled trait.
PHYLIP
PHYLogenetic Inference Package (pronounced fy-lip).
phylogenetic tree
A graphic representation of the phylogeny of a group of taxa or genes.
phylogenetics
The reconstruction of the evolutionary history of a group of taxa or genes.
phylogeny
The evolutionary history of a group of taxa or genes and their ancestors.
plasmid
An autonomous, self-replicating extrachromosomal circular DNA.
plesiomorphy
A shared ancestral character state.
point mutation
A mutation affecting only one nucleotide site. Usually, in reference to a nucleotide substitution.
polarity
The property of nucleic acids to be read one way from 5' to 3' and differently in the opposite direction.
polyadenylation signal
A box on most eukaryotic mRNA molecules that specifies the location of the polyadenylation site.
polyadenylation site (poly(A)-addition site)
The 3' end of most mRNA molecules in eukaryotes. The site at which a poly-A tail is added.
polygamy
A mating system in which a male mates with more than one female (polygyny) or a female mates with more than one male (polyandry)
polymorphism (genetic polymorphism)
The coexistence of two or more alleles at a locus.
polypeptide
A molecule made of amino acids covalently linked to each other by peptide bonds. Often, a term used to denote the amino acid chain of a protein before it assumes a functional three-dimensional configuration.
polyphyletic
Descended from different ancestors.
polyploidy (genome doubling, genome duplication)
The presence in a cell or an individual of more than two haploid sets of chromosomes (e.g., tetraploidy, hexaploidy).
population
A group of individuals in a species that share a common gene pool.
population size (census population size)
The number of individuals in a population.
positive selection
Selection for an advantageous mutant allele.
posterior probability
The probability of a parameter value inferred from an analysis.
pre-messenger RNA (pre-mRNA)
The primary transcript of a protein-coding gene before maturation.
preproprotein
The primary product of translation before any posttranslational changes have been made.
pretermination codon
A codon that requires only one mutation to become a termination codon.
primary amino acid
One of the 20 amino acids specified by the universal genetic code.
primary structure
The sequence of amino acids in a polypeptide chain. The sequence of nucleotides in a DNA or RNA molecule.
prior probability
The probability of a parameter value at the start of an analysis.
processed gene
(see retrogene)
progressive alignment
An heuristic method for multiple sequence alignment wherein pairwise alignments are made of progressively less closely related sequences. These methods use a guide tree from an clustering method, such as neighbor-joining, as a starting point for pairwise comparison.
proprotein
A product of translation after the signal peptide has been removed and before additional posttranslational modifications have been made.
prosthetic group
A nonprotein molecule attached to an apoprotein that is required for functionality (e.g., heme in hemoglobin).
protein
A molecule composed of one or more polypeptide chains. May or may not contain prosthetic groups.
protein-coding gene
A gene that contains a reading frame, the mRNA of which is translated.
provirus
A viral genome integrated into the genome of the host cell.
pseudogene
A functionless segment of DNA exhibiting sequence homology to a functional gene. A nonfunctional member of a gene family.
purifying selection (negative selection)
A selection regime resulting in the removal of an allele from the population.
purine
A type of nitrogen base present in nucleotides and composed of two joined ring structures, one five-membered and one six-membered. The purine bases in DNA and RNA are adenine and guanine.
pyrimidine
A type of nitrogen base present in nucleotides and composed of a single six-membered ring. The pyrimidine bases in DNA are cytosine and thymine. The pyrimidine bases in RNA are cytosine and uracil.