Everything about Sequence database

🧭 Start here: a 6-step reading path

1. Read the overview: Sequence databaseA 5-minute orientation
2. Skim a recent paper: AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequencesInfluential work since 2022
3. Pick up a classic book: BioinformaticsThe most-reprinted book on the subject
4. Read the landmark paper: The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interestCited 10,462 times
5. Go sideways: European Bioinformatics InstituteA closely related topic
6. Go sideways: BioinformaticsA closely related topic

🏆 Landmark papers (most cited)

• The STRING database in 2023: protein–protein association networks and functional enrichment analyses for any sequenced genome of interest

  Damian Szklarczyk, Rebecca Kirsch, Mikaela Koutrouli · 2022 · Nucleic Acids Research · 10,462 citations

• AlphaFold Protein Structure Database: massively expanding the structural coverage of protein-sequence space with high-accuracy models

  Mihaly Varadi, Stephen Anyango, Mandar Deshpande · 2021 · Nucleic Acids Research · 8,427 citations

• PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences

  M. Lescot · 2002 · Nucleic Acids Research · 7,437 citations

• Introducing EzBioCloud: a taxonomically united database of 16S rRNA gene sequences and whole-genome assemblies

  Seok-Hwan Yoon, Sung-Min Ha, Soonjae Kwon · 2017 · International Journal of Systematic and Evolutionary Microbiology · 7,223 citations

• Probability-based protein identification by searching sequence databases using mass spectrometry data

  David N. Perkins, Darryl J. C. Pappin, David M. Creasy · 1999 · Electrophoresis · 6,929 citations

• Reference sequence (RefSeq) database at NCBI: current status, taxonomic expansion, and functional annotation

  Nuala A. O'Leary, Mathew W. Wright, J. Rodney Brister · 2015 · Nucleic Acids Research · 6,361 citations

• An approach to correlate tandem mass spectral data of peptides with amino acid sequences in a protein database

  Jimmy K. Eng, Ashley L. McCormack, John R. Yates · 1994 · Journal of the American Society for Mass Spectrometry · 5,825 citations

🆕 Influential since 2022

• AlphaFold Protein Structure Database in 2024: providing structure coverage for over 214 million protein sequences

  Mihaly Varadi, Damian Bertoni, Paulyna Magana · 2023 · Nucleic Acids Research · 2,364 citations

• The UNITE database for molecular identification and taxonomic communication of fungi and other eukaryotes: sequences, taxa and classifications reconsidered

  Kessy Abarenkov, R Henrik Nilsson, Karl-Henrik Larsson · 2023 · Nucleic Acids Research · 979 citations

• The IPD-IMGT/HLA database: recent developments in sequence submission

  Dominic J Barker, Richard H L Natarajan, Michael A Cooper · 2025 · Nucleic Acids Research · 186 citations

• The antiSMASH database version 4: additional genomes and BGCs, new sequence-based searches and more

  Kai Blin, Simon Shaw, Marnix H Medema · 2023 · Nucleic Acids Research · 134 citations

• Considerations for constructing a protein sequence database for metaproteomics

  J. Alfredo Blakeley-Ruiz, Manuel Kleiner · 2022 · Computational and Structural Biotechnology Journal · 92 citations

📚 Books worth reading

• BioinformaticsAndreas D. Baxevanis, B. F. Francis Ouellette · 2001
• Introduction to bioinformaticsStephen A. Krawetz, David D. Womble · 2002
• Database annotation in molecular biologyArthur M. Lesk · 2005
• Genetic DatabasesO. Corrigan · 2004
• Introduction to bioinformaticsArthur M. Lesk · 2002
• Gene function analysisMichael F. Ochs · 2007
• BLASTIan Korf · 2003
• RNA and DNA editingRuslan Aphasizhev · 2011

Ranked by number of editions on Open Library, a rough measure of how lasting a book is.

🔗 Related topics

• European Bioinformatics Institute The European Bioinformatics Institute (EMBL-EBI) is an intergovernmental organization (IGO) which, as part of the European Molecular Biology Laboratory…
• Bioinformatics Bioinformatics (/ˌbaɪ.oʊˌɪnfərˈmætɪks/ ) is an interdisciplinary field of science that develops computational methods and software tools for understanding…
• UniProt UniProt is a freely accessible database of protein sequence and functional information, many entries being derived from genome sequencing projects. It…
• Computational genomics Computational genomics refers to the use of computational and statistical analysis to decipher biology from genome sequences and related data, including…
• Sequence analysis In bioinformatics, sequence analysis is the process of subjecting a DNA, RNA or peptide sequence to any of a wide range of analytical methods to understand…
• Sequence alignment In bioinformatics, a sequence alignment is a way of arranging the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence…
• BioJava BioJava is an open-source software project dedicated to providing Java tools for processing biological data. BioJava is a set of library functions written…
• Protein family A protein family is a group of evolutionarily related proteins. In many cases, a protein family has a corresponding gene family, in which each gene encodes…