Bioinformatics Glossary
This glossary provides definitions for common terms used in bioinformatics and computational biology. Understanding these terms is essential for navigating the field and communicating effectively with collaborators.
Genetics and Biology Concepts
Gene
A region of DNA that encodes a functional product, such as a protein or functional RNA.
Allele
One of multiple alternative versions of a gene at a specific genomic location.
Genotype
The genetic makeup of an organism, defined by the variants it carries.
Phenotype
The observable traits or characteristics of an organism resulting from its genotype and environment.
Mutation
A change in DNA sequence that may affect gene function.
Genome Editing
The deliberate modification of DNA sequences using targeted molecular tools (e.g., CRISPR-Cas9).
Computational Context
Bioinformatics
The application of computational methods to analyze and interpret biological data.
Pipeline / Workflow
An ordered sequence of computational steps that transform raw data into biological results.
Method
A computational or experimental approach used to analyze biological data.
Core Sequencing and Data Terms
Sequencing
The laboratory process of determining the order of nucleotides (A, C, G, T or U) in DNA or RNA molecules.
Sequencing Reads (Reads)
Short nucleotide sequences produced by a sequencing machine that represent fragments of the original DNA or RNA.
FASTQ File
A standard file format that stores sequencing reads together with a quality score for each nucleotide.
Quality Score (Base Quality)
A numerical estimate of how confident the sequencing machine is that a given nucleotide was read correctly. Typically encoded as Phred quality scores.
Coverage / Depth
The average number of reads that align to (or "cover") each base in a reference sequence. Higher coverage generally leads to more confident variant calls or assemblies.
Reference-Based Analysis Terms
Reference Genome
A curated representative genome sequence used as a coordinate system for aligning and analyzing sequencing data.
Mapping (Alignment)
The process of assigning sequencing reads to their most likely positions on a reference genome.
Mapping Quality
A measure of how confident the algorithm is that a sequencing read was aligned to the correct genomic location.
SAM / BAM File
File formats that store aligned sequencing reads and their associated quality information. SAM (Sequence Alignment/Map) is text-based, while BAM is a compressed binary version.
Variant
A difference in DNA sequence between a sample and a reference genome.
Single Nucleotide Variant (SNV)
A variant affecting a single nucleotide position in the genome.
Single Nucleotide Polymorphism (SNP)
An SNV that is common within a population (typically >1% frequency).
Insertion / Deletion (Indel)
A variant where one or more nucleotides are inserted into or deleted from the genome.
Variant Calling
The computational process of identifying genetic variants from aligned sequencing reads.
Variant Call Format (VCF)
A standardized file format that stores detected genetic variants along with supporting evidence and quality metrics.
De Novo Analysis and Assembly Terms
De Novo Analysis
A type of analysis that reconstructs genome sequences directly from sequencing reads without using a reference genome.
Genome Assembly
The process of combining overlapping sequencing reads into longer continuous sequences.
Contig
A continuous DNA sequence assembled from overlapping sequencing reads (contiguous sequence).
Scaffold
A set of ordered and oriented contigs that approximate larger genomic regions, often containing gaps.
N50
A statistic indicating that 50% of the total assembly length is contained in contigs of this length or longer. Higher N50 values indicate better assemblies.
FASTA File
A simple text-based file format for storing nucleotide or protein sequences without quality information.
Genome Annotation
The process of identifying genes and other functional elements within a genome sequence.
Metagenomics Terms
Metagenomics
The study of genetic material obtained directly from mixed communities of organisms in a single sample.
Metagenome
The combined genetic content of all organisms present in a metagenomic sample.
Binning
The process of grouping assembled sequences that are likely to originate from the same organism.
Metagenome-Assembled Genome (MAG)
A draft genome reconstructed from metagenomic data through assembly and binning.
Taxonomic Profiling
The identification and quantification of organisms present in a biological sample.
Functional Profiling
The identification of genes and metabolic pathways encoded by a biological community.
Microbiome
The collection of microorganisms (bacteria, fungi, viruses) living in a specific environment, such as the human gut.
Transcriptomics Terms
Transcriptomics
The study of all RNA molecules expressed in a cell, tissue, or organism at a given time.
RNA-seq
A sequencing method used to measure RNA abundance and gene expression levels.
Transcriptome
The complete set of RNA transcripts produced by a genome under specific conditions.
Gene Expression
The process by which genetic information is used to produce RNA and proteins. In the context of RNA-seq, it refers to the abundance of RNA transcripts.
Expression Quantification
The measurement of how frequently each gene or transcript is observed in sequencing data.
Differential Expression Analysis
A statistical analysis that identifies genes whose expression levels differ significantly between conditions or sample groups.
Expression Matrix
A table containing gene or transcript expression values across multiple samples (rows = genes, columns = samples).
TPM (Transcripts Per Million)
A normalized measure of gene expression that accounts for both sequencing depth and gene length.
FPKM / RPKM
Fragments/Reads Per Kilobase of transcript per Million mapped reads. Older normalization methods for RNA-seq data.
File Formats
FASTA
Text format for nucleotide or protein sequences. Each sequence starts with a header line (beginning with >) followed by the sequence.
FASTQ
Extension of FASTA that includes quality scores for each base. Standard output format from sequencing machines.
SAM/BAM
Sequence Alignment/Map format for storing aligned reads. BAM is the compressed binary version.
VCF/BCF
Variant Call Format for storing genetic variants. BCF is the compressed binary version.
GFF3/GTF
Gene annotation formats describing genomic features (genes, exons, etc.).
BED
Browser Extensible Data format for genomic intervals and annotations.
HDF5
Hierarchical Data Format for storing large, complex datasets, commonly used in single-cell sequencing.
Statistical and Analysis Terms
P-value
The probability of observing results as extreme as those obtained, assuming the null hypothesis is true.
Adjusted P-value (FDR, padj)
P-value corrected for multiple testing to control the false discovery rate.
Log2 Fold Change
A measure of how much a gene's expression has changed between conditions, on a log2 scale. A value of 1 means doubled expression, -1 means halved.
Principal Component Analysis (PCA)
A dimensionality reduction technique used to visualize similarities and differences between samples.
Clustering
Grouping samples or genes with similar characteristics or expression patterns.
Ontologies and Databases
Ontology
A controlled vocabulary of terms and their relationships, used to standardize biological knowledge.
Gene Ontology (GO)
A standardized system for describing gene function, cellular component, and biological process.
BLAST
Basic Local Alignment Search Tool - algorithm for comparing sequences to find regions of similarity.
NCBI
National Center for Biotechnology Information - major database of biological sequences and literature.
UniProt
Universal Protein Resource - comprehensive protein sequence and functional information database.
Ensembl
Genome browser and annotation database for vertebrate and other eukaryotic genomes.
Quality Control Terms
PHRED Score
Quality score representing the probability that a base call is incorrect. Score of 20 = 1% error rate, 30 = 0.1% error rate.
Adapter Contamination
Sequencing artifacts where adapter sequences from library preparation are present in reads.
PCR Duplicates
Identical reads arising from PCR amplification during library preparation rather than independent sequencing events.
GC Content
The percentage of guanine (G) and cytosine (C) bases in a sequence, which can affect sequencing quality.
Additional Resources
For more detailed information on bioinformatics terminology:
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