Reference health

The EMBL-EBI bioinformatics web and programmatic tools framework

37/37 checkable references clean · checked 2026-07-22

Every reference with a DOI in the deposited reference list resolved to a known work in Crossref or DataCite at the dated check, and none carried a retraction, withdrawal, or removal notice.

The 37 checked references that resolve

resolves10.1093/nar/gkt1206

The European Bioinformatics Institute’s data resources 2014

resolves10.1093/nar/gkq313

A new bioinformatics analysis tools framework at EMBL-EBI

resolves10.1093/nar/gkt376

Analysis Tool Web Services from the EMBL-EBI

resolves10.1186/1471-2105-10-421

BLAST+: architecture and applications

resolves10.1093/bioinformatics/bts240

PSI-Search: iterative HOE-reduced profile SSEARCH searching

resolves10.1093/bioinformatics/btu031

InterProScan 5: genome-scale protein function classification

resolves10.1186/1471-2105-8-298

Predicting active site residue annotations in the Pfam database

resolves10.1038/msb.2011.75

Fast, scalable generation of high‐quality protein multiple sequence alignments using Clustal Omega

resolves10.1093/nar/gkn1006

Kalign2: high-performance multiple alignment of protein and nucleotide sequences allowing external features

resolves10.1093/molbev/mst010

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

resolves10.1093/nar/gku1129

Content discovery and retrieval services at the European Nucleotide Archive

resolves10.1093/nar/gkt979

Ensembl Genomes 2013: scaling up access to genome-wide data

resolves10.1093/nar/gku989

UniProt: a hub for protein information

resolves10.1093/nar/gku1243

The InterPro protein families database: the classification resource after 15 years

resolves10.1093/nar/gkt1223

Pfam: the protein families database

resolves10.1002/0471250953.bi0312s48

Using EMBL‐EBI Services via Web Interface and Programmatically via Web Services

resolves10.1093/bib/bbp065

Fast and efficient searching of biological data resources--using EB-eye

resolves10.1093/bioinformatics/btt509

Infernal 1.1: 100-fold faster RNA homology searches

resolves10.1186/1471-2105-11-133

MapMi: automated mapping of microRNA loci

resolves10.1002/0471142727.mb1911s96

Phylogenetic Analysis of Protein Sequence Data Using the Randomized Axelerated Maximum Likelihood (<scp>RAXML</scp>) Program

resolves10.4161/worm.19574

WormBase

resolves10.1093/nar/gks1005

Rfam 11.0: 10 years of RNA families

resolves10.1016/S0076-6879(96)66010-8

[8] SRS: Information retrieval system for molecular biology data banks

resolves10.1093/nar/gki442

InterProScan: protein domains identifier

resolves10.1093/nar/gkh111

HGVbase: a curated resource describing human DNA variation and phenotype relationships

resolves10.1002/pmic.200300721

The International Protein Index: An integrated database for proteomics experiments

resolves10.1093/bioinformatics/btm404

Clustal W and Clustal X version 2.0

resolves10.1073/pnas.85.8.2444

Improved tools for biological sequence comparison.

resolves10.1093/bioinformatics/btt100

BioJS: an open source JavaScript framework for biological data visualization

resolves10.1093/nar/gkt263

Challenges in homology search: HMMER3 and convergent evolution of coiled-coil regions

resolves10.1093/nar/gkn174

R-Coffee: a method for multiple alignment of non-coding RNA

resolves10.1093/nar/gku1010

Ensembl 2015

resolves10.1093/bioinformatics/16.6.566

DaliLite workbench for protein structure comparison

resolves10.1093/nar/28.15.2919

DbClustal: rapid and reliable global multiple alignments of protein sequences detected by database searches

resolves10.1016/0022-2836(91)90883-8

Database algorithm for generating protein backbone and side-chain co-ordinates from a Cα trace

resolves10.1002/0471250953.bia01es00

Sequence File Format Conversion with Command‐Line Readseq

resolves10.1093/nar/gkg573

WU-Blast2 server at the European Bioinformatics Institute

What this badge says. CiteStamped means the CHECKABLE references of this work were clean at the dated check: each resolved to a known work in a public registry, and none carried a retraction notice at that time. It says nothing about the quality, findings, or importance of the work itself, and nothing about references deposited without a DOI.

checked 2026-07-22 — re-checked daily as this page is visited; titles and statuses come from Crossref and DataCite and are not part of the signed record

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