Introduction to Bioinformatics, Genome Sequencing and Alignment

Key terms and definitions from Sections A, B, and C of the Bioinformatics Revision Workbook covering foundational concepts, sequencing techniques, and alignment algorithms.

Bioinformatics

The application of computer science, mathematics and statistics to collect, store, analyse and interpret biological data.

Genome

The complete DNA sequence of an organism.

Gene

A sequence of DNA that contains the information to produce a functional RNA or protein.

Sequence

The order of nucleotides in DNA/RNA or amino acids in a protein.

Genomics

The study of an organism's complete genome.

Transcriptomics

The study of all RNA molecules produced by a cell or organism.

Proteomics

The study of all proteins produced by a cell or organism.

Database

A collection of biological information that can be searched and analysed.

NCBI

A public database containing DNA, RNA, protein, genome and biomedical literature.

UniProt

A database of protein sequences and functional information.

PDB (Protein Data Bank)

A database containing three-dimensional protein structures.

Ensembl

A genome browser providing annotated genome information for many species.

DNA Sequencing

Determining the exact order of nucleotides in a DNA molecule.

Sanger Sequencing

A first-generation sequencing method using chain-terminating nucleotides.

Next-Generation Sequencing (NGS)

High-throughput sequencing technology capable of sequencing millions of DNA fragments simultaneously.

Whole Genome Shotgun Sequencing (WGS)

Sequencing method where DNA is randomly fragmented and computationally assembled.

Read

A short DNA sequence generated by a sequencing machine.

Contig

A continuous DNA sequence assembled from overlapping reads.

Scaffold

A group of ordered contigs linked using additional sequencing information.

Genome Assembly

The process of reconstructing a genome from sequencing reads.

Coverage (Depth)

The average number of times each nucleotide has been sequenced.

N50

Assembly statistic where $50\%$ of the genome is contained in contigs of that length or longer.

Paired-End Sequencing

Sequencing both ends of a DNA fragment.

Mate-Pair Sequencing

Sequencing distant ends of long DNA fragments to improve scaffolding.

Sequence Alignment

The process of comparing sequences to identify similarities and differences.

Pairwise Alignment

Alignment of two sequences.

Global Alignment

Alignment across the entire length of two sequences.

Local Alignment

Alignment of only the most similar regions.

Needleman-Wunsch Algorithm

Dynamic programming algorithm for global alignment.

Smith-Waterman Algorithm

Dynamic programming algorithm for local alignment.

Dynamic Programming

Method that finds the optimal alignment by scoring all possibilities.

Gap Penalty

Score deducted when gaps are introduced into an alignment.

Scoring Matrix

Matrix assigning scores to matches, mismatches and substitutions.

PAM Matrix

Substitution matrix used for closely related proteins.

BLOSUM Matrix

Substitution matrix commonly used for more divergent protein sequences.