The probability of an alignment occurring with the score in
question or better. The p value is calculated by relating the
observed alignment score, S, to the expected distribution of
HSP scores from comparisons of random sequences of the same
length and composition as the query to the database. The most
highly significant P values will be those close to 0. P values
and E values are different ways of representing the significance
of the alignment. (NCBI)
P1-derived artificial chromosome (PAC)
One type of vector used to clone DNA fragments (100- to 300-kb
insert size; average, 150 kb) in Escherichia coli cells. Based
on bacteriophage (a virus) P1 genome.
See also: cloning vector
(ORNL)
PAM
Point Accepted Mutation. A unit introduced by Dayhoff et al.
to quantify the amount of evolutionary change in a protein sequence.
1.0 PAM unit, is the amount of evolution which will change,
on average, 1% of amino acids in a protein sequence. A PAM(x)
substitution matrix is a look-up table in which scores for each
amino acid substitution have been calculated based on the frequency
of that substitution in closely related proteins that have experienced
a certain amount (x) of evolutionary divergence. (NCBI)
Paralogous
Homologous sequences within a single species that arose by
gene duplication. (NCBI)
Partly open barrel
Has the edge strands not properly hydrogen bonded because
one of the strands is in two parts connected with a linker of
more than than one residue. These edge strands can be treated
as a single but interrupted strand, allowing classification
with the effective strand and shear numbers, n* and S*. In the
few open barrels the beta sheets are connected by only a few
side-chain hydrogen bonds between the edge strands. (SCOP)
In genetics, conferring the right or title to genes, gene
variations, or identifiable portions of sequenced genetic
material to an individual or organization.
See also: gene (ORNL)
Pedigree
A family tree diagram that shows how a particular genetic
trait or disease has been inherited.
See also: inherit (ORNL)
Penetrance
The probability of a gene or genetic trait being expressed.
"Complete" penetrance means the gene or genes for
a trait are expressed in all the population who have the genes.
"Incomplete" penetrance means the genetic trait is
expressed in only part of the population. The percent penetrance
also may change with the age range of the population. (ORNL)
Peptide
Two or more amino acids joined by a bond called a "peptide
bond."
See also: polypeptide (ORNL)
A map of the locations of identifiable landmarks on DNA (e.g.,
restriction-enzyme cutting sites, genes), regardless of inheritance.
Distance is measured in base pairs. For the human genome, the
lowest-resolution physical map is the banding patterns on the
24 different chromosomes; the highest-resolution map is the
complete nucleotide sequence of the chromosomes. (ORNL)
Plasmid
Autonomously replicating extra-chromosomal circular DNA molecules,
distinct from the normal bacterial genome and nonessential for
cell survival under nonselective conditions. Some plasmids are
capable of integrating into the host genome. A number of artificially
constructed plasmids are used as cloning vectors. (ORNL)
Pleiotropy
One gene that causes many different physical traits such as
multiple disease symptoms. (ORNL)
Pluripotency
The potential of a cell to develop into more than one type
of mature cell, depending on environment. (ORNL)
Genetic disorder resulting from the combined action of alleles
of more than one gene (e.g., heart disease, diabetes, and
some cancers). Although such disorders are inherited, they
depend on the simultaneous presence of several alleles; thus
the hereditary patterns usually are more complex than those
of single-gene disorders.
See also: single-gene disorder
(ORNL)
Polymerase chain reaction (PCR)
A method for amplifying a DNA base sequence using a heat-stable
polymerase and two 20-base primers, one complementary to the
(+) strand at one end of the sequence to be amplified and one
complementary to the (-) strand at the other end. Because the
newly synthesized DNA strands can subsequently serve as additional
templates for the same primer sequences, successive rounds of
primer annealing, strand elongation, and dissociation produce
rapid and highly specific amplification of the desired sequence.
PCR also can be used to detect the existence of the defined
sequence in a DNA sample. (ORNL)
Polymerase, DNA or RNA
Enzyme that catalyzes the synthesis of nucleic acids on preexisting
nucleic acid templates, assembling RNA from ribonucleotides
or DNA from deoxyribonucleotides. (ORNL)
Difference in DNA sequence among individuals that may underlie
differences in health. Genetic variations occurring in more
than 1% of a population would be considered useful polymorphisms
for genetic linkage analysis.
See also: mutation (ORNL)
Single-stranded DNA or RNA molecules of specific base sequence,
labeled either radioactively or immunologically, that are used
to detect the complementary base sequence by hybridization.
(ORNL)
Profile
A table that lists the frequencies of each amino acid in each
position of protein sequence. Frequencies are calculated from
multiple alignments of sequences containing a domain of interest.
See also PSSM. (NCBI)
A profile is a table of position-specific scores and gap penalties,
representing an homologous family, that may be used to search
sequence databases. In CLUSTAL-W-derived profiles those sequences
that are more distantly related are assigned higher weights.
(SMART)
Cell or organism lacking a membrane-bound, structurally discrete
nucleus and other subcellular compartments. Bacteria are examples
of prokaryotes.
See also: chromosome, eukaryote
(ORNL)
Promoter
A DNA site to which RNA polymerase will bind and initiate
transcription. (ORNL)
Pronucleus
The nucleus of a sperm or egg prior to fertilization.
See also: nucleus, transgenic
(ORNL)
A large molecule composed of one or more chains of amino acids
in a specific order; the order is determined by the base sequence
of nucleotides in the gene that codes for the protein. Proteins
are required for the structure, function, and regulation of
the body's cells, tissues, and organs; and each protein has
unique functions. Examples are hormones, enzymes, and antibodies.
(ORNL)
Proteome
Proteins expressed by a cell or organ at a particular time
and under specific conditions. (ORNL)
Proteomics
Systematic analysis of protein expression of normal and diseased
tissues that involves the separation, identification and characterization
of all of the proteins in an organism. (NCBI)
Pseudogene
A sequence of DNA similar to a gene but nonfunctional; probably
the remnant of a once-functional gene that accumulated mutations.
(ORNL)
PSI-BLAST
Position-Specific Iterative BLAST. An iterative search using
the BLAST algorithm. A profile is built after the initial search,
which is then used in subsequent searches. The process may be
repeated, if desired with new sequences found in each cycle
used to refine the profile. Details can be found in this discussion
of PSI-BLAST. (Altschul et al.) (NCBI)
PSSM
Position-specific scoring matrix; see profile.
The PSSM gives the log-odds score for finding a particular matching
amino acid in a target sequence. (NCBI)
Purine
A nitrogen-containing, double-ring, basic compound that occurs
in nucleic acids. The purines in DNA and RNA are adenine and
guanine.
See also: base pair (ORNL)
Pyrimidine
A nitrogen-containing, single-ring, basic compound that occurs
in nucleic acids. The pyrimidines in DNA are cytosine and
thymine; in RNA, cytosine and uracil.
See also: base pair (ORNL)
