Glossary Molecular Biology and Computational Biology

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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.

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