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Genomics – Terminologies
Open reading frame – A region of a DNA sequence, of reasonable
length, that begins with an initiate codon (ATG) and ends with a stop
codon. It is a potential protein coding region.
SNP – Single nu cleotide polimorphism. It is a si ngle base variation,
between genomes, involving isolated substitutions at individual
positions.
Haplotype – A local combin ation of genetic polymorphisms that tend
to be co-inheritted, or inherited as a block.
CRISPR / Cas – Is a defence mechanism to protect prokaryotes against
viral infections, but has been modified to edit genomes of eukaryotes,
in cluding hu mans, in the laboratory.
Co ntig – The parti al assembly of data from overlapping fragme nts in
order to form a adjacent region of sequence.
Sequence asse mbly – Gathering the complete sequence of a DNA
strand by piecing together the overlaps between individual fragments.
Sequence co verage - The number of bases sequenced (in a project)
over the genome length. The average number of times the base
appears in the sequence reads.
Single-end read – The determination of the nu cleotide se quence from
only one end of a template DNA molecule.
Paired-end read – The determination of a nucleotide sequence from
both ends of a templ ate DNA mol ecule.
De novo sequencing – Determining the full-ge nome sequence without
using a known reference sequence from an individu al of the species.
Re sequencing - Determining the sequence of an indi vidual of a
species f or which a reference genome sequence is already known.
Exome sequencing – Sequencing of protein coding regions (exon s) in
a genome in oder to identify the geneti c origin of a lesion which causes
an inheri ted disease.
Transposons – Are mobile DNA elements that transpose
(transfer/move) by cutting themselves out of the inserted area ab d
in sert themselves el sewhere in the gen ome.
, Retrotransposon – Are mobile D NA elements that transpose by
making copies if themselves and inserting the copies elsewhere in the
genome, with the original copy still at the original location.
Re striction fragme nts – A fragment of the DNA mole cule that has
been cleaved by a restricti on enzyme. The restriction enzyme is used to
cut DNA into smaller fragments, be cause the enzyme is designed to
make the cut at a specific nucleotide sequence or restriction si te.
Re striction map – It is a map of known restri ction sites within a DNA
sequence. It is used to map an unknown segment of DNA by breaking it
in to smaller pieces and then identifying the locations as breakpoints.
VNTR – Vari able number tandem repeat. It i s a location on the genome
where short nucleotide sequen ces are organized as a tandem repeat.
They can be found on many chromosomes and variations in lengths are
shown be tween different individuals.
RFLP – Restriction fragment length polymorphism. The vari ation in the
length of a restriction fragme nt produced by a restri ction enzyme
acting on DNA from different individual s that usal ly result from a
genetic mutation, that can be used as a genetic marker.
STR – Short Tandem Repeats. Occurs in DNA when a pattern of two or
more nucle otide s are repe ated and the repeated sequences are directly
adjacent to one another. It is also known as a microsattelite. The
pattern can range in leng th from 2 -16 bp and is typically in a non-
coding intron region.
Linkage – It is a phe nomon on that entails anal ysing the distri bution of
genes or loci along chromosomes.
Linkage disequilibrium – A phenomonon that entails the measuring of
the distribution of allelic patterns in populations.
C-value – Used to refer to the amount of DNA in a haploi d cell, that is,
a gamete. The letter C refers to the constancy of the smount of DNA
per cell in a species.
Homologue s – Refers to a gene that is related to another gene by
descent from a common ancestral DNA sequence. Applies to the
rel ationship betwe en genes that were seperated by an event of
speciation or to the relationship between genes seperated by an event
of geneti c duplicati on.
Orthologues – Are genes in different species that evolved from a
common ancestral gen e through the proce ss of speciation. These gene
perform the same fun ction in different species.
Paralogues – Related genes that have diverged from one another to
provide separate functions in the same species.
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