Biological Databases & Websites Overview

A collection of flashcards focusing on key terms and definitions related to biological databases and bioinformatics.

FASTA format

A text-based format for representing nucleotide or peptide sequences, where sequences are preceded by a header line.

FASTQ format

A file format for storing both a biological sequence and its corresponding quality scores, typically used in sequencing data.

NCBI (National Center for Biotechnology Information)

A US government agency that provides access to biomedical and genomic information.

GenBank

A primary database of nucleotide sequences maintained by NCBI.

XML (Extensible Markup Language)

A markup language that defines rules for encoding documents in a format that is both human-readable and machine-readable.

Entrez

NCBI’s search and retrieval system that provides a unified interface to multiple databases.

RefSeq

A curated and non-redundant database of reference sequences for genomes, transcripts, and proteins.

Genome browser

A web-based tool that visualizes genomic data along with annotations and features.

Metadata

Data that provides information about other data, often used to describe the characteristics of biological sequences.

ASCII files

Text files that contain data represented in a format readable by humans and includes sequence data.

SNP (Single Nucleotide Polymorphism)

A variation at a single position in a DNA sequence among individuals.

Public repositories

Databases that hold biological data accessible to the public, including NCBI, EBI, and DDBJ.

Biological Process (Gene Ontology)

A larger process accomplished by multiple molecular activities.

Cellular Component (Gene Ontology)

Locations relative to cellular structures where functions are performed.

Molecular Function (Gene Ontology)

Activities that occur at the molecular level, such as enzyme activity or binding.

Gene Ontology (GO)

A collaborative project that aims to standardize the representation of gene and gene product attributes.

Biological Sequence Databases

Databases that store and provide access to biological sequences.

Unix Server

A powerful computer system utilized for hosting and processing large-scale bioinformatics data.

Programming utilities

Software tools provided by database hosts to facilitate bulk data access.

Quality values in FASTQ

Encoded error probability values that represent the reliability of sequence data.

BioProject

An NCBI database that organizes data associated with a biological research project.

BLAST (Basic Local Alignment Search Tool)

A tool that finds similarities between biological sequences.

Genome Workbench

An integrated software suite for studying and analyzing genetic data.

MarkerDB

A database consolidating information on clinical and pre-clinical biomarkers.

DRUGBANK

A comprehensive resource for drug discovery that integrates various biomedical data.

Genome Data Viewer

A tool provided by NCBI to visualize and explore genomic data.

Proteomics

The large-scale study of proteins, particularly their functions and structures.

Taxonomy

The science of classifying and naming organisms.

Gene ID

A unique identifier assigned to a gene for reference in various databases.

Entrez Help Manual

A guide that provides instructions on using NCBI's Entrez system.

Clinical significance

The importance of a specific genetic variant in terms of its influence on health.

SRA (Sequence Read Archive)

A database that stores raw sequencing data and related information.

EBI (European Bioinformatics Institute)

An organization that provides freely available data and services in bioinformatics.

DDBJ (DNA Data Bank of Japan)

A database that collects and disseminates nucleotide sequence data.

PubMed

A free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics.

Clinical trials

Research studies performed on patients to evaluate a medical, surgical, or behavioral intervention.

Unique identifier (SeqID)

A distinct code used to label biological sequences in databases.

Common languages in bioinformatics

Typically include programming languages such as Python and R for data analysis.

Open reading frame (ORF)

A sequence of DNA that can be translated to give a protein.

Accession number

A unique identifier assigned to a biological sequence record in a database.

Submission Portal (NCBI)

An online entry point for submitting data to various NCBI databases.