Bioinformatic Terms
Alignment
The juxtaposition of residues between two or more sequences along with gaps that models the evolutionary or functional changes between the sequences . Alignments can be global (showing the changes across the entire lengths of the sequences) or local (showing only the changes within the most conserved area of the sequences).
Annotation
Adding pertinent information such as gene coded for, amino acid sequence, or
other commentary to the database entry of raw sequence of DNA bases.
Autosome
A chromosome not involved in sex determination. The diploid human genome
consists of a total of 46 chromosomes: 22 pairs of autosomes, and 1 pair of sex
chromosomes (the X and Y chromosomes).
Bacterial artificial chromosome (BAC)
A vector used to clone DNA fragments (100- to 300-kb insert size; average,
150 kb) in Escherichia coli cells. Based on naturally occurring F-factor plasmid
found in the bacterium E. coli.
BLAST
A computer program that identifies homologous (similar) genes in different
organisms, such as human, fruit fly, or nematode.
Candidate gene
A gene located in a chromosome region suspected of being involved in a
disease.
Deletion
A loss of part of the DNA from a chromosome; can lead to a disease or
abnormality.
Expressed sequence tag (EST)
A short strand of DNA that is a part of a cDNA molecule and can act as
identifier of a gene. Used in locating and mapping genes.
Functional genomics
The study of genes, their resulting proteins, and the role played by the proteins
in the body's biochemical processes.
Gene chip technology
Development of cDNA microarrays from a large number of genes. Used to
monitor and measure changes in gene expression for each gene represented on
the chip.
Homology
Similarity in DNA or protein sequences between individuals of the same
species or among different species.
Insertion
A chromosome abnormality in which a piece of DNA is incorporated into a
gene and thereby disrupts the gene's normal function.
See also: chromosome, DNA, gene, mutation
Knockout
Deactivation of specific genes via specific DNA binding mechanisms;
used in laboratory organisms to study gene function.
Locus (pl. loci)
The position on a chromosome of a gene or other chromosome marker; also,
the DNA at that position. The use of locus is sometimes restricted to mean
expressed DNA regions.
Mutagen
An agent that causes a permanent genetic change in a cell. Does not include
changes occurring during normal genetic recombination.
Northern blot
A gel-based laboratory procedure that locates mRNA sequences on a gel that
are complementary to a piece of DNA used as a probe.
Operon
A set of genes transcribed under the control of an operator gene.
Physical map
A map of the locations of identifiable landmarks on DNA (e.g., restrictionenzyme
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.
Pleiotropy
One gene that causes many different physical traits such as multiple disease
symptoms.
Primer
Short preexisting polynucleotide chain to which new deoxyribonucleotides can
be added by DNA polymerase.
Probe
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.
Promoter
A DNA site to which RNA polymerase will bind and initiate transcription.
Proteome
Proteins expressed by a cell or organ at a particular time and under specific
conditions.
Proteomics
The study of the full set of proteins encoded by a genome.
Recombinant DNA technology
Procedure used to join together DNA segments in a cell-free system (an
environment outside a cell or organism). Under appropriate conditions, a
recombinant DNA molecule can enter a cell and replicate there, either
autonomously or after it has become integrated into a cellular chromosome.
Sanger sequencing
A widely used method of determining the order of bases in DNA.
See also: sequencing, shotgun sequencing
Scaffold
In genomic mapping, a series of contigs that are in the right order but not
necessarily connected in one continuous stretch of sequence.
Sequence assembly
A process whereby the order of multiple sequenced DNA fragments is
determined.
Sequencing
Determination of the order of nucleotides (base sequences) in a DNA or RNA
molecule or the order of amino acids in a protein.
Sequencing technology
The instrumentation and procedures used to determine the order of nucleotides
in DNA.
Shotgun method
Sequencing method that involves randomly sequenced cloned pieces of the
genome, with no foreknowledge of where the piece originally came from. This
can be contrasted with "directed" strategies, in which pieces of DNA from known
chromosomal locations are sequenced. Because there are advantages to both
strategies, researchers use both random (or shotgun) and directed strategies in
combination to sequence the human genome.
Translocation
A mutation in which a large segment of one chromosome breaks off and
attaches to another chromosome.
Uracil
A nitrogenous base normally found in RNA but not DNA; uracil is capable of
forming a base pair with adenine.
Virus
A noncellular biological entity that can reproduce only within a host cell.
Viruses consist of nucleic acid covered by protein; some animal viruses are also
surrounded by membrane. Inside the infected cell, the virus uses the synthetic
capability of the host to produce progeny virus.
Western blot
A technique used to identify and locate proteins based on their ability to bind
to specific antibodies.
Xenograft
Tissue or organs from an individual of one species transplanted into or grafted
onto an organism of another species, genus, or family. A common example is the
use of pig heart valves in humans.
Yeast artificial chromosome (YAC)
Constructed from yeast DNA, it is a vector used to clone large DNA
fragments.
See also: cloning vector, cosmid
Zinc-finger protein
A secondary feature of some proteins containing a zinc atom; a DNA-binding
protein.
