Genomics Glossary for DNA Sequencing | Discovering the Genome

base pairs (bp)	Paired nucleotides that make up DNA and RNA. Following specific hydrogen-bonding patterns, DNA has adenine(A)-thymine(T) and guanine(G)-cytosine(C) base pairings. Similarly, RNA has adenine-uracil(U) and guanine-cytosine base pairings
chromosome	a single molecule of DNA that is highly organized (by proteins) when cells divide. When cells are not dividing, this single molecule of DNA is less structured
complementary strands (of DNA)	two single opposing stands of DNA that bind as a result of base pairing throughout their full length
deoxyribonucleic acid (DNA)	the molecule that encodes the information for all the characteristics or traits about an organism
DNA polymerase	a protein enzyme that helps synthesize new strings of DNA by copying an existing string
DNA Sequencing	“Reading” the DNA molecule to determine the sequence of the letters
flow cell	a special glass plate that is a little larger than a microscope slide, which is used to attach DNA or cDNA (made from RNA) samples to sequence them in next-generation sequencing machines
gene expression	the process by which instructions in our DNA are converted into functional products, such as proteins (read more about the basics of gene expression)
genome	all the DNA in an organism
genomics	the study of a large number of genes and their interactions and/or of entire genomes (all of the DNA in an organism) to learn what kind of information is coded in these DNA sequences and how the DNA instructions are carried out
mutation	alterations in the DNA
nucleotides	the basic structural units of nucleic acids such as DNA and RNA. They are made up of a nucleoside coupled to a phosphate group
parallel sequencing	any of several high-throughput and next-generation sequencing approaches to DNA sequencing that are able to process a very large number of sequencing reactions at the same time
primer	short nucleotide sequences that serve as a starting point for DNA synthesis. They are required for DNA replication because DNA polymerase can only add nucleotides to an existing DNA strand.
proteins	large complex molecules that perform many critical roles for an organism to function
read alignment, read mapping	The entire process of taking sequencing reads and assigning them to specific locations in the genome
sequence motif	a particular string of nucleotides whose pattern is repeated at least once in a long string that is related to the function of a gene
sequencing	The process of determining the order of nucleotides that makes up DNA or RNA
spatial indexing	a technique used in next-generation sequencing machines that uses the position of strings of DNA on the flow cell to help sequence the strings more quickly
stem cells	unspecialized cells that are capable of dividing and renewing themselves for long periods (self-renewal) as well as give rise to specialized cells. Different stem cell types have different limitations as to what type of specialized cells they can differentiate into.
string	a sequence of one or more letters