SCH2141 Advanced Biomedical Techniques - Bioinformatics Laboratories

Vocabulary practice flashcards covering bioinformatics concepts, online tools (NCBI BLAST, Clustal Omega, NEBcutter, GeneCards, EMBOSS Transeq, EMBOSS Cpgplot, JSmol), sequence formats, and analysis methods from the SCH2141 Advanced Biomedical Techniques laboratory sessions.

Chromatogram Nucleotide Peak Colors

The color-coding convention used in sequencing chromatograms where Green represents Adenine, Red represents Thymine, Blue represents Cytosine, and Black represents Guanine.

'N' (Chromatogram Call)

A base call designation indicating that the automated sequencing program is unable to determine which specific nucleotide is present at that position.

Chromas

A software application used to view sequence chromatograms and inspect, edit, find, or replace nucleotides.

GOLD Sequence

The verified and edited nucleotide sequence obtained directly from an individual's sequencing chromatogram, saved in FASTA format.

FASTA Format

A text-based sequence format beginning with a greater-than symbol ($>$) followed by header information, with sequence lines formatted without spaces at $60\text{ bp}$ per line.

BLAST (Basic Local Alignment Search Tool)

An NCBI program that identifies regions of similarity between biological sequences by comparing a nucleotide or protein query against databases and calculating statistical significance.

Subject (BLAST Alignment)

The database match sequence against which the query sequence is compared and aligned in a standard BLAST result output.

Coding Sequence (CDS)

The specific range of nucleotides in a gene transcript that directly encodes the amino acid sequence of a protein, positioned between start and stop codons.

Clustal Omega

A multiple sequence alignment program from EMBL-EBI that uses seeded guide trees and HMM profile-profile techniques to align three or more nucleotide or protein sequences.

Asterisk (*) in Clustal Omega

A consensus symbol indicating positions where identical nucleotides or amino acids are completely conserved across all aligned sequences.

INDEL

An insertion or deletion event evidenced in sequence alignments where one or more nucleotides or amino acids are missing or inserted relative to homologous sequences.

Single Nucleotide Polymorphism (SNP)

A single base or amino acid substitution occurring at a specific homologous position between compared biological sequences.

NEBcutter

A restriction endonuclease analysis tool provided by New England BioLabs that identifies restriction sites and generates restriction maps for submitted DNA sequences.

1 Cutter

A restriction enzyme that recognizes and cleaves a target DNA sequence at exactly one position.

GeneCards

A comprehensive, searchable integrative human gene database integrating genomic, transcriptomic, proteomic, genetic, and clinical information from approximately $125$ web sources.

rs-number

A standardized reference identifier used in genetic databases to designate a specific Single Nucleotide Polymorphism (SNP) variant.

HomoloGene

An NCBI database that detects and presents curated putative homologous gene sets across diverse eukaryotic organisms.

EMBOSS Transeq

An EMBL-EBI sequence analysis tool that translates nucleotide sequences into corresponding peptide sequences across up to $6$ reading frames simultaneously.

Reading Frame

One of six possible ways ($3$ forward and $3$ reverse) of reading a double-stranded nucleotide sequence as a non-overlapping series of triplet codons.

Asterisk (*) in EMBOSS Transeq

A character denoting a translation stop codon, which terminates the open reading frame.

EMBOSS Cpgplot

An EMBL-EBI tool used to calculate sequence statistics, identify, and plot putative CpG islands based on GC percentage and observed-versus-expected CpG ratios.

CpG Island

A genomic region containing a high frequency of Cytosine and Guanine dinucleotides exceeding an expected baseline threshold of $50\%\text{ GC}$.

JSmol

A non-Java, JavaScript-based molecular viewer that enables interactive 3D visualization and manipulation of macromolecules directly inside web browsers.