Bioinformatics Glossary
Core vocabulary for bioinformatics and computational biology — from sequence alignment and BLAST to genome assembly and variant calling.
Run BLAST search →Bioinformatics
The interdisciplinary field combining biology, computer science, and statistics to analyze and interpret biological data.
Read definition →BLAST
Basic Local Alignment Search Tool — the standard algorithm for comparing nucleotide or protein sequences against databases.
Read definition →BLAST Specificity
The ability of BLAST to distinguish true homologs from false-positive matches, controlled by E-value thresholds.
Read definition →E-value
Expect value — the number of alignments with equal or better score expected by chance in a database search.
Read definition →Alignment
The arrangement of sequences to identify regions of similarity, indicating functional or evolutionary relationships.
Read definition →Genome Assembly
The process of reconstructing a complete genome from overlapping DNA fragments sequenced by NGS platforms.
Read definition →Variant Calling
Identifying differences between a sample genome and a reference, including SNPs, indels, and structural variants.
Read definition →SNP
Single Nucleotide Polymorphism — a single-base variation at a specific genomic position, the most common type of genetic variation.
Read definition →SNP Filtering
Quality-based filtering of called variants using metrics like read depth, mapping quality, and strand bias.
Read definition →ClinVar
NCBI database of human genetic variants and their clinical significance, classifying variants as pathogenic, benign, or uncertain.
Read definition →dbSNP
NCBI database cataloging short genetic variations (SNPs, indels) and their chromosomal locations across organisms.
Read definition →Haplotype
A group of alleles on a single chromosome that are inherited together, often used to trace evolutionary lineages.
Read definition →Phylogeny
The evolutionary history and relationships among organisms or genes, represented as a branching tree diagram.
Read definition →Bowtie2 Alignment
A fast and memory-efficient tool for aligning sequencing reads to long reference sequences using FM-index.
Read definition →Illumina
The dominant short-read sequencing platform using sequencing-by-synthesis chemistry with fluorescently labeled reversible terminators.
Read definition →Oxford Nanopore
A long-read sequencing technology that measures ionic current changes as DNA passes through protein nanopores.
Read definition →FASTQ
The standard file format storing raw sequencing reads and their corresponding quality scores from NGS instruments.
Read definition →BAM
Binary Alignment/Map — the compressed binary format for storing aligned sequencing reads against a reference genome.
Read definition →VCF
Variant Call Format — the standard file format for storing gene sequence variations including SNPs, indels, and structural variants.
Read definition →Next-generation Sequencing
High-throughput DNA sequencing technologies that parallelize the sequencing process to produce millions of reads simultaneously.
Read definition →Metagenomics
The study of genetic material recovered directly from environmental samples, characterizing microbial communities without culturing.
Read definition →Ensembl
A genome browser and annotation database providing reference genomes, gene models, and comparative genomics for vertebrates.
Read definition →Machine Learning
Algorithms that improve performance on tasks through experience and data, increasingly used for variant calling and structure prediction.
Read definition →Deep Learning
A subset of ML using multi-layered neural networks for pattern recognition in genomics, protein structure, and drug discovery.
Read definition →NCBI
National Center for Biotechnology Information — the primary US repository for genomic data, literature, and bioinformatics tools.
Read definition →Repeat Masking
Identifying and masking repetitive DNA sequences (SINEs, LINEs, transposons) to improve alignment and annotation accuracy.
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