Reference health

NCBI BLAST + integrated into Galaxy

https://doi.org/10.1101/014043
CiteStamped reference-health badge
1 of 31 checkable references need attention · checked 2026-07-25

At the dated check, the references listed below either did not resolve in Crossref or DataCite, or carried a retraction notice. Each one is shown with the registry record that put it there.

1 without a DOI — not checked. A reference deposited without a DOI is never matched by title or guessed at; it stays outside the checked set, and this line discloses that.

References needing attention

does not resolve to a known work10.1006/jmbi.1990.9999
The 30 checked references that resolve
resolves10.1101/gr.361602
The Bioperl Toolkit: Perl Modules for the Life Sciences
resolves10.1093/bioinformatics/btp163
Biopython: freely available Python tools for computational molecular biology and bioinformatics
resolves10.1093/bioinformatics/btn397
BioJava: an open-source framework for bioinformatics
resolves10.1093/bioinformatics/btq475
BioRuby: bioinformatics software for the Ruby programming language
resolves10.1186/gb-2010-11-8-r86
Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
resolves10.1002/0471142727.mb1910s89
Galaxy: A Web‐Based Genome Analysis Tool for Experimentalists
resolves10.1093/nar/gkq429
myExperiment: a repository and social network for the sharing of bioinformatics workflows
resolves10.1186/gb4161
Dissemination of scientific software with Galaxy ToolShed
resolves10.7717/peerj.167
Galaxy tools and workflows for sequence analysis with applications in molecular plant pathology
resolves10.1093/nar/gku365
deepTools: a flexible platform for exploring deep-sequencing data
resolves10.1186/2041-1480-4-2
OPPL-Galaxy, a Galaxy tool for enhancing ontology exploitation as part of bioinformatics workflows
resolves10.1093/bioinformatics/btu135
Orione, a web-based framework for NGS analysis in microbiology
resolves10.1186/1471-2105-11-S12-S4
Galaxy CloudMan: delivering cloud compute clusters
resolves10.1093/bioinformatics/btt501
TALENoffer: genome-wide TALEN off-target prediction
resolves10.1186/1471-2105-10-421
BLAST+: architecture and applications
resolves10.1093/bioinformatics/btr010
A novel hybrid gene prediction method employing protein multiple sequence alignments
resolves10.1093/bioinformatics/btm009
Identifying bacterial genes and endosymbiont DNA with Glimmer
resolves10.1093/bioinformatics/btu153
Prokka: rapid prokaryotic genome annotation
resolves10.3389/fgene.2013.00237
Blobology: exploring raw genome data for contaminants, symbionts and parasites using taxon-annotated GC-coverage plots
resolves10.1002/biot.201000181
Prokaryotic gene clusters: A rich toolbox for synthetic biology
resolves10.1021/ja501630w
Regio- and Stereoselective Intermolecular Oxidative Phenol Coupling in <i>Streptomyces</i>
resolves10.1021/pr500812t
Flexible and Accessible Workflows for Improved Proteogenomic Analysis Using the Galaxy Framework
resolves10.1093/nar/gkp1137
The Sanger FASTQ file format for sequences with quality scores, and the Solexa/Illumina FASTQ variants
resolves10.5281/zenodo.15781
docker-galaxy-blast: The NCBI Blast+ 2.2.29 release
resolves10.1093/bioinformatics/btu119
Wrangling Galaxy’s reference data
resolves10.1093/nar/25.17.3389
Gapped BLAST and PSI-BLAST: a new generation of protein database search programs
resolves10.1093/nar/29.14.2994
Improving the accuracy of PSI-BLAST protein database searches with composition-based statistics and other refinements
resolves10.1093/nar/gkh454
CD-Search: protein domain annotations on the fly
resolves10.1093/nar/gkq769
Allotopic expression of mitochondrial-encoded genes in mammals: achieved goal, undemonstrated mechanism or impossible task?
resolves10.1186/1471-2164-14-397
Web-based visual analysis for high-throughput genomics
The 1 reference without a DOI — listed, not checked
no DOI — not checkedYong, E. : There’s No Plague on the NYC Subway. No Platypuses Either. National Geographic Magazine, Phenomena: Not Exactly Rocket Science (2015). http://phenomena.nationalgeographic.com/2015/02/10/theres-no-plague-on-the-nyc-subway-no-platypuses-either/
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 2026-07-25 — 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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