Research Guides: BIOL 301L: Genetics Lab: Databases

Welcome!

This course guide is for students in Prof. Garrison's BIOL-301L Genetics Lab completing the "Decoding Genomes" research assignment. Below please find a selection of resources for researching genes, genomes, and nucleotide sequences, including National Center for Biotechnology Information (NCBI) databases. If you have any questions, please don't hesitate to contact the librarians.

Article Databases

PubMed Medline This link opens in a new window
Provides access to over 34 million citations from MEDLINE and other life science journals for biomedical articles back to the 1950s. Includes links to many sites providing full text articles and other related resources.
Web of Science This link opens in a new window
Unified search of Arts & Humanities, Science, and Social Sciences Citation Indexes. Indexes and abstracts more than 10,000 major scholarly journals. Provides the number of times cited and links to those articles, as well as full bibliographies. Mobile: new interface optimized for mobile users.
Library Search This link opens in a new window
Library Search is an easy but powerful way to access nearly all of our information resources (including our book holdings, Web of Science, Project Muse and more) from a single search box. Mobile-friendly; devices are automatically detected.

Genetics resources and sequence databases

Selected National Center for Biotechnology Information (NCBI) databases

NCBI Assembly
A database providing information on the structure of assembled genomes, assembly names and other metadata, statistical reports, and links to genomic sequence data.
NCBI Basic Local Alignment Search Tool (BLAST)
BLAST finds regions of similarity between biological sequences. The program compares nucleotide or protein sequences to sequence databases and calculates the statistical significance.
NCBI Gene
Gene integrates information from a wide range of species. A record may include nomenclature, Reference Sequences (RefSeqs), maps, pathways, variations, phenotypes, and links to genome-, phenotype-, and locus-specific resources worldwide.
NCBI Genome
Organizes information on genomes including sequences, maps, chromosomes, assemblies, and annotations
NCBI Nucleotide
The Nucleotide database is a collection of sequences from several sources, including GenBank, RefSeq, TPA and PDB. Genome, gene and transcript sequence data provide the foundation for biomedical research and discovery.
NCBI RefSeq: Reference Sequence Database
A comprehensive, integrated, non-redundant, well-annotated set of reference sequences including genomic, transcript, and protein sequences.
NCBI Taxonomy
A curated classification and nomenclature for all of the organisms in the public sequence databases. This currently represents about 10% of the described species of life on the planet.

Tips and more information for using the above NCBI databases

NCBI Assembly:

An assembly is a genomic sequence resulting from the reassembly of sequenced chromosome fragments. The NCBI Assembly database was created by NCBI to handle the complex organization of genomes. Search options include by organism name (e.g. homo sapiens (humans)), assembly accession number (e.g. GCA_000001405.28), or assembly name or synonym (e.g. GRch38), or browse by organism.

Additional Resources

Online Mendelian Inheritance in Man (OMIM)
An online catalog of human genes and genetic disorders.
Vertebrate Genomes Project
The goal of the VGP is to generate near error-free reference genome assemblies of all 66,000 extant vertebrate species.
Ensembl
A genome browser for vertebrate genomes that supports research in comparative genomics, evolution, sequence variation and transcriptional regulation. Ensembl annotate genes, computes multiple alignments, predicts regulatory function and collects disease data.

BIOL 301L: Genetics Lab

BIOL 301L: Genetics library lab handout

Science Librarian