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Molecular Biology and Computational Biology Glossary
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(Continued from previous part...)
Sanger sequencing
A widely used method of determining the order of bases in
DNA.
Satellite
A chromosomal segment that branches off from the rest of the
chromosome but is still connected by a thin filament or stalk.
Scaffold
In genomic mapping, a series of contigs that are in the right
order but not necessarily connected in one continuous stretch
of sequence.
Seed Alignment
Alignment that contains only one of each pair of homologues
that are represented in a CLUSTALW-derived phylogenetic tree
linked by a branch of length less than a distance of 0.2 (see
the related article).
SEG
A program for filtering low complexity regions in amino acid
sequences. Residues that have been masked are represented as
"X" in an alignment. SEG filtering is performed by
default in the blastp subroutine of BLAST 2.0. (Wootton and
Federhen)
Segregation
The normal biological process whereby the two pieces of a
chromosome pair are separated during meiosis and randomly distributed
to the germ cells.
Sequence
Sequence assembly
A process whereby the order of multiple sequenced DNA fragments
is determined.
Sequence
tagged site (STS)
Short (200 to 500 base pairs) DNA sequence that has a single
occurrence in the human genome and whose location and base sequence
are known. Detectable by polymerase chain reaction, STSs are
useful for localizing and orienting the mapping and sequence
data reported from many different laboratories and serve as
landmarks on the developing physical map of the human genome.
Expressed sequence tags (ESTs) are STSs derived from cDNAs.
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. )
Sex chromosome
The X or Y chromosome in human beings that determines the
sex of an individual. Females have two X chromosomes in diploid
cells; males have an X and a Y chromosome. The sex chromosomes
comprise the 23rd chromosome pair in a karyotype.
Traits or diseases associated with the X or Y chromosome;
generally seen in males.
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.
Similarity
The extent to which nucleotide or protein sequences are related.
The extent of similarity between two sequences can be based
on percent sequence identity and/or conservation. In BLAST similarity
refers to a positive matrix score. (
Single nucleotide polymorphism (SNP)
DNA sequence variations that occur when a single nucleotide
(A, T, C, or G) in the genome sequence is altered.
Single-gene
disorder
Hereditary disorder caused by a mutant allele of a single
gene (e.g., Duchenne muscular dystrophy, retinoblastoma, sickle
cell disease).
Somatic cell
Any cell in the body except gametes and their precursors.
Somatic
cell gene therapy
Incorporating new genetic material into cells for therapeutic
purposes. The new genetic material cannot be passed to offspring.
Somatic cell
genetic mutation
A change in the genetic structure that is neither inherited
nor passed to offspring. Also called acquired mutations.
Southern
blotting
Transfer by absorption of DNA fragments separated in electrophoretic
gels to membrane filters for detection of specific base sequences
by radio-labeled complementary probes.
Spectral karyotype (SKY)
A graphic of all an organism's chromosomes, each labeled with
a different color. Useful for identifying chromosomal abnormalities.
Splice site
Location in the DNA sequence where RNA removes the noncoding
areas to form a continuous gene transcript for translation into
a protein. )
Sporadic cancer
Cancer that occurs randomly and is not inherited from parents.
Caused by DNA changes in one cell that grows and divides,
spreading throughout the body.
Stem cell
Undifferentiated, primitive cells in the bone marrow that
have the ability both to multiply and to differentiate into
specific blood cells.
Structural genomics
The effort to determine the 3D structures of large numbers
of proteins using both experimental techniques and computer
simulation
Substitution
The presence of a non-identical amino acid at a given position
in an alignment. If the aligned residues have similar physico-chemical
properties the substitution is said to be "conservative".
Substitution
In genetics, a type of mutation due to replacement of one
nucleotide in a DNA sequence by another nucleotide or replacement
of one amino acid in a protein by another amino acid.
Substitution Matrix
A substitution matrix containing values proportional to the
probability that amino acid i mutates into amino acid j for
all pairs of amino acids. such matrices are constructed by assembling
a large and diverse sample of verified pairwise alignments of
amino acids. If the sample is large enough to be statistically
significant, the resulting matrices should reflect the true
probabilities of mutations occuring through a period of evolution.
Suppressor gene
A gene that can suppress the action of another gene.
Syndrome
The group or recognizable pattern of symptoms or abnormalities
that indicate a particular trait or disease.
Syngeneic
Genetically identical members of the same species.
Synteny
Genes occurring in the same order on chromosomes of different
species.
(Continued on next part...)
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