MCDB 30H Definitions & Terms

alignment

a way to arrange 2+ sequences to identify regions of similarity

barcode

the sequence used to muliplex sequence fragments (With multiplex sequencing, individual "barcode" sequences are added to each DNA fragment during next-generation sequencing (NGS) library preparation so that each read can be identified and sorted before the final data analysis. These barcodes, or index adapters, can follow one of two major indexing strategies depending on your library prep kit and application.)

bioinformatics

multidisciplinary science that applies math, CS, statistics to understand biological info on a large scale

BLAST

Basic local alignment search tool...performs local alignment, statistical significance of matches; finds potential matches of one sequence of interest against all known sequences

Bowtie

software developed to quickly perform local alignment of many short sequences (usually sequencing reads) against a larger sequence (often an entire genome)

Cufflinks

Software developed to assemble transcrip ts from short RNA-sequencing reads

Demultiplex

Use barcodes to separate sequence reads into the corresponding samples

FASTA

file format produced by next-generation sequencing technologies that shows all sequence reads

FASTQ

file format produced by next-generation sequencing technologies that shows all sequence reads AND corresponding quality values

Global alignment

alignment of entire sequences

Illumina

biotech company, and a specific next-generation sequencing technology that emphasizes number of sequence reads at the expense of read length

Local alignment

Alignment of a portion of one sequence to the entirety of another sequence

Multiplex

Allows multiple samples to be run concurrently by adding a short nucleotide sequencing onto each fragment based on sample

Next-generation sequencing

collection of technologies that allow for quicker & cheaper sequencing than what was previously available

Paired-end read

Two reads are generated per DNA or RNA fragment, one from the 5' end and one from the 3' end

Read

Result of sequencing experiment; single ordered set of nucleotides derived from a fragment of DNA or RNA

Sequencing

Process to determine nucleotide order of a fragment of DNA or RNA

Sequencing coverage

Average number of reads that align to a position in the genome (mathematically equivalent to the number of reads that align to the genom/read length/genome size)

Sequencing error

When sequencing technology miscalls a base in a sequencing read

Single end-read

A single read is generated per DNA or RNA fragment

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