ABT – Computational Test Review: Bioinformatics Tools, Sequence Analysis, and Gene Characterization

Vocabulary practice flashcards covering chromatogram analysis, BLAST alignment metrics, multiple sequence alignments (Clustal Omega), restriction enzyme analysis (NEBcutter), reading frame translation (EMBOSS Transeq), CpG island detection (EMBOSS CpGplot), and NCBI/GeneCards genetic resources.

Chromatogram

A visual representation of a DNA sequence using coloured peaks that correspond to individual nucleotides.

Chromatogram base color coding

The standard fluorescent color scheme for sequencing traces: Adenine (A) is Green, Thymine (T) is Red, Cytosine (C) is Blue, and Guanine (G) is Black.

Ambiguous base call (N)

A position where the sequencing software cannot confidently identify the nucleotide base.

Chromas

A bioinformatics program that displays and allows editing of DNA sequencing chromatogram files, identifying nucleotide sequences (A, T, C, G) and ambiguous bases (N).

NCBI Nucleotide BLAST

A bioinformatics tool that compares a DNA sequence in FASTA format against sequences in a database to identify the most likely matching gene, species, percentage identity, and sequence location.

Percent identity (BLAST)

The proportion of aligned nucleotides that match between the query and target sequences.

Query coverage (BLAST)

A metric indicating how much of the submitted sequence is represented in the alignment.

E-value (Expect value)

A BLAST statistic indicating how likely a match of that quality would occur by chance, where a smaller value indicates a more significant match.

Gaps (BLAST)

Insertions or deletions represented in an alignment between two or more sequences.

NCBI Nucleotide / Protein

An NCBI database resource that provides reference DNA, RNA, and protein sequences in FASTA format, along with associated sequence information, searched via gene name or accession number.

Clustal Omega

A multiple sequence alignment program that aligns two or more DNA or protein sequences in FASTA format to identify conserved regions, substitutions, and possible INDELs.

Asterisk (* in Clustal Omega)

An alignment symbol indicating that all aligned sequences have the same nucleotide or amino acid ($100\%$ identical, fully conserved homologous column).

Colon (: in Clustal Omega)

A protein alignment symbol indicating strongly similar amino acid properties with a score greater than $0.5$.

Period (. in Clustal Omega)

A protein alignment symbol indicating weakly similar amino acid properties with a score less than or equal to $0.5$.

Hyphen (- in Clustal Omega)

An alignment symbol denoting an indel (insertion or deletion) or a gap introduced during sequence alignment.

Single Nucleotide Polymorphism (SNP)

A single-nucleotide variation occurring at a particular genomic position.

INDEL

An insertion or deletion of one or more nucleotides within a DNA sequence.

Synonymous substitution

A nucleotide change that does not alter the encoded amino acid.

Non-synonymous substitution

A nucleotide change that alters the encoded amino acid.

Conserved region

A sequence stretch displaying high sequence similarity, potentially indicating evolutionary or functional importance.

NEBcutter

A web-based tool that identifies restriction enzyme recognition and cutting sites in a FASTA DNA sequence, showing which enzymes cut, cleavage locations, cut frequencies, and whether blunt or sticky ends are generated.

GeneCards

A searchable database that provides detailed information about a gene, including molecular function, tissue expression, chromosomal location, associated disorders, and genetic variants.

NCBI dbSNP

A database providing information about known genetic variants, SNP positions, alternative alleles, and available allele frequency data using a gene name or rs identifier.

NCBI HomoloGene

An NCBI resource that identifies homologous genes across different species, displaying genes with shared evolutionary ancestry.

NCBI Gene

An NCBI database providing information about gene structure and location, identifying chromosome assignment, exon and intron positions, gene architecture, and associated sequences.

Exon

A region of a gene that is retained in mature RNA.

Intron

A non-coding region of a gene that is removed during RNA splicing.

Homologous genes

Genes that share evolutionary ancestry and may exhibit similar sequences or functions across different species.

EMBOSS Transeq

A translation tool that translates nucleotide sequences into amino acid sequences across six reading frames, allowing identification of the likely protein-coding open reading frame.

Six reading frames

The six possible translation registers of double-stranded DNA, comprising three forward reading frames on one strand and three reverse-complement frames on the opposite strand.

NCBI Pairwise BLAST

A BLAST tool that aligns two nucleotide sequences to identify matching regions, nucleotide positions, mismatches, and gaps.

CpG island

A DNA region with a relatively high frequency of CpG dinucleotides, often associated with gene regulatory regions such as promoters.

EMBOSS CpGplot

A bioinformatics program that analyzes a FASTA nucleotide sequence to detect and plot potential CpG islands with elevated CpG content.