Bioinformatics Workshop Flashcards

Flashcards covering key terms, databases, and tools introduced in the bioinformatics workshop including BLAST, Ensembl, and PCR primer design.

Bioinformatics

A range of approaches and tools used to analyse and interpret biological data, including genetic sequences, protein structures, and 'omics' data.

BLAST (Basic Local Alignment Search Tool)

A tool that enables the comparison of different sequences, such as genetic or amino acid sequences, to identify functional domains or predict gene function.

GeneCards

A database of all human genes, including protein coding information, gene structure, sequence variants, transcripts, and expression in different tissues.

Online Mendelian Inheritance in Man (OMIM)

A compendium of all known inherited disorders containing information on genetic basis and clinical features, with entries for $15,831$ genes and $5,182$ phenotypes.

Genome Browsers

Bioinformatics tools, such as Ensembl and UCSC, that enable data from a variety of sources to be collated and displayed graphically.

Ensembl

A comprehensive genome browser established by the European Bioinformatics Institute (EBI) and the Wellcome Trust Sanger Center covering humans, animals, plants, bacteria, and fungi.

Track

In a genome browser, a separate horizontal line used to display specific genomic features like genes, variants, or regulatory elements.

UCSC Genome Browser

A bioinformatics tool known for being intuitive and easy to navigate, used to obtain sequences surrounding mutations and localise transcripts.

Polymerase Chain Reaction (PCR)

A fundamental molecular biology technique used to amplify a specific, small region of DNA.

Primers

Short oligonucleotides, designated as 'forward' and 'reverse,' that 'bookend' a specific DNA region to enable amplification.

Low E-value

A value in BLAST results indicating that the sequence alignment found is unlikely to be due to chance.

CFTR (Cystic Fibrosis Transmembrane Conductance Regulator)

A member of the ATP-binding cassette (ABC) transporter superfamily that functions as a chloride channel; mutations in this gene cause cystic fibrosis.

DeltaF508

The most common mutation involved in cystic fibrosis, resulting in impaired folding and trafficking of the CFTR protein.

Primer3

A web-based tool (version $4.1.0$) used to pick primers from a DNA sequence by establishing parameters like melting temperature ($ext{tm}$) and GC percentage.