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The University of Massachusetts Amherst


A guide to resources in Biology at UMass and beyond.

From the National Center for Biotechnology Information

From the NCBI website: "Established in 1988 as a national resource for molecular biology information, NCBI creates public databases, conducts research in computational biology, develops software tools for analyzing genome data, and disseminates biomedical information..."

Entrez Nucleotide
A collection of sequences from several sources, including GenBank, RefSeq, and PDB.

Protein sequences
Compiled from a variety of sources, including SwissProt, PIR, PRF, PDB, and translations from annotated coding regions in GenBank and RefSeq.

Genome database
Provides views for a variety of genomes, complete chromosomes, sequence maps with contigs, and integrated genetic and physical maps.

Molecular Modeling Database (MMDB)
Contains over 40,000 3D macromolecular structures, including proteins and polynucleotides. It's linked to the rest of the NCBI databases, including sequences, bibliographic citations, taxonomic classifications, and sequence and structure neighbors.

Other Databases and Tools

a collection of 14,728 Pathway/Genome Databases (PGDBs), plus software tools for exploring them [Karp17]. Key aspects of BioCyc data:

  • Quality data curated from tens of thousands of publications, including curated databases for E. coli, B. subtilis, H. sapiens, and S. cerevisiae.
  • Computationally predicted metabolic pathways and operons.
  • Data integrated from other databases including gene essentiality, regulatory networks, protein features, and GO annotations.

UCSC Genome Browser at the University of California Santa Cruz

Nucleic Acid Database at Rutgers University