DNA Sequencing Flashcards
DNA Sequence Information
The order of nucleotides in the DNA molecule
Maxam-Gilbert Sequencing
A chemical sequencing method based on controlled breakage of DNA.
Sanger Sequencing
A modification of the DNA replication process. Dideoxy chain termination sequencing.
Dideoxy Chain Termination Method
Sanger Method. A method using dideoxynucleotides to determine the order or sequence of nucleotides in a nucleic acid.
Internal Labeling
Incorporation of radioactive nucleotides in chain termination sequencing for visualization of the sequencing ladder.
ddNTP
Dideoxynucleotide. Causes the new DNA chain to terminate due to the lack of the hydroxyl group found on the 3’ ribose carbon.
M13 Universal Primer
A sequencing primer that could be used for all sequences cloned into the M13 RF plasmid.
Dye Blobs
Bright flashes of fluorescence caused by failure to clean the sequencing ladder properly.
Dye Primer
Covalent attachment of fluorescent molecules to a sequencing primer.
Dye Terminator
Covalent attachment of fluorescent molecules to dideoxynucleotides.
Electropherogram
Results from capillary electrophoresis where fluorescent signals are recorded as graphical peaks.
Dye Blobs
Artifactual peak pattern caused by risidual unincorporated labeled dideoxynucleotides in a sequencing reaction. Bright flashes of fluorescence.
Pyrosequencing
A method designed to determine a DNA sequence without having to make a sequencing ladder. Based on the release of pyrophosphates during DNA replication.
Pyrogram
The results from a pyrosequencing reaction that consist of peaks of luminescence associated with the addition of the complementary nucleotide from a pyrosequencer.
Bisulfite DNA Sequencing
Methylation-specific sequencing. Chain termination sequencing designed to detect methylated cytosine nucleotides. DNA has been treated with sodium bisulfite.
Polonies
Collection of products of fragments that hybridized to the immobilized probes that were amplified by branch PCR.
Indexing
Bar coding. Adaptors that contain short sequences, 6-8 bases, that will identify the sample, allowing multiple samples to be sequenced together.
Bioinformatics
The merger of biology with information technology.
in silico
By computer
Annotation
Classification of sequence variants based on their biological and/or clinical significance.
Consensus Sequences
A family of sequences.
Filtering
Selection of variants found in a sequence based on variant features such as variant frequency, coverage, exon, or intron location, germline/somatic status, or other properties.
Bioinformatics
The merger of biology with information technology.
in silico
Analysis performed by computer
M13
A single-stranded DNA bacteriophage used in early procedures to make single-stranded templates for sequence analysis.
Consensus Sequences
A family of sequences representing different variations in a population but with similar motifs in nucleotide order.
BLAST
The Basic Local Alignment Search Tool. A system for homology searches. Compares nucleotide or protein sequences to find regions of similarity between them.
Homology
Having the same.
Sequencing by Synthesis
Involves taking a single strand of the DNA to be sequenced and then synthesizing its complementary strand enzymatically, one base at a time.
Reversible Terminator Sequencing
A sequencing approach that relies on solid-phase amplification of DNA templates immobilized to a solid surface (usually a flow cells) separated across it to generate clusters on the order of millions.
Bridge Amplification
A double stranded DNA is denatured so that each strand can separately attach to an oligonucleotide sequence anchored to the flow cell. One will be the reverse strand; the other, the forward.
Flow Cell
An Illumina flow cell is a hollow glass slide with one or more channels (“lanes”), coated with oligonucleotides which are complementary to the sequencing adapters so that single-stranded, adapter-ligated DNA fragments can attach through hybridization.
