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Insignia specifications


Unique identifier OMICS_14277
Name Insignia
Interface Web user interface
Restrictions to use None
Input data Any set of target and background genomes selected from the online database.
Output data A list of signatures perfectly conserved by all target genomes and absent from all of the background genomes.
Programming languages C++, Javascript, Perl, PHP
Computer skills Basic
Stability No
Maintained No



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Publication for Insignia

Insignia citations


HTSFinder: Powerful Pipeline of DNA Signature Discovery by Parallel and Distributed Computing

Evol Bioinform Online
PMCID: 4750899
PMID: 26884678
DOI: 10.4137/EBO.S35545

[…] the signatures.The additional challenge as another major limitation for DNA signature discovery methods is the lack of option in the choice of target and nontarget genome databases. TOFI, TOPSI, and Insignia use BLAST databases (such as nt and nr databases) for the background or nontarget genomes for specificity evaluation of signatures and there is no option for the user to choose other target a […]


DNA Sequence Signatures for Rapid Detection of Six Target Bacterial Pathogens Using PCR Assays

PMCID: 4515919
PMID: 26279626
DOI: 10.4137/MBI.S29736

[…] natures in assay development, the processes for selecting DNA signatures have generally not been well described in the literature.,In our previous study, we established a computational workflow using Insignia, dCAS, and NCBI-BlastN sequentially for the identification of DNA signatures from whole genome sequence data that can be used as the basis for designing real-time PCR assays using Streptococc […]


Development of Real Time PCR Array for Simultaneous Detection of Eight Human Blood Borne Viral Pathogens

PLoS One
PMCID: 3422334
PMID: 22912836
DOI: 10.1371/journal.pone.0043246

[…] We used the “Insignia” program (, a bioinformatics on line tool developed in the Center for Bioinformatics and Computational Biology, University of Maryland to choose a spec […]


Evolutionary and Experimental Assessment of Novel Markers for Detection of Xanthomonas euvesicatoria in Plant Samples

PLoS One
PMCID: 3359998
PMID: 22655073
DOI: 10.1371/journal.pone.0037836

[…] The draft genome sequences of Xv, Xg and Xp, that were recently made available , will certainly contribute to a more reliable prediction of specific regions for the different BSX species by CUPID and Insignia. A BLAST analysis carried out with the NCBI whole-genome shotgun contigs (wgs) database allowed to extend the in silico specificity tests to include these draft genomes. In accordance with th […]


Alignment Free Design of Highly Discriminatory Diagnostic Primer Sets for Escherichia coli O104:H4 Outbreak Strains

PLoS One
PMCID: 3320637
PMID: 22496820
DOI: 10.1371/journal.pone.0034498

[…] ularly computationally intensive due to the whole genome alignment step. This has a heavy scaling penalty when more than a small number of genomes are aligned that is avoided by methods such as TOFI, Insignia, and ssGeneFinder, by the use of pairwise genome alignment or progressive sequence subtraction, which is computationally more efficient , , , . However, as has been noted elsewhere , TOFI and […]


A parallel and incremental algorithm for efficient unique signature discovery on DNA databases

BMC Bioinformatics
PMCID: 2848650
PMID: 20230647
DOI: 10.1186/1471-2105-11-132

[…] matics algorithms to determine horizontally transferred, pathotype-specific signature genes as targets for specific, high-throughput molecular diagnostic applications and reverse vaccinology screens; insignia [] is a web application for rapidly identifying unique DNA signatures, and hybseek [] is a web service for efficiently designing both pathogen-specific and compatible primer pairs for DNA-bas […]

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Insignia institution(s)
Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD, USA; Department of Biochemistry and Molecular & Cellular Biology, Georgetown University Medical Center, WA, DC, USA
Insignia funding source(s)
This work was supported by US Department of Homeland Security Science and Technology Directorate under award NBCH2070002 in part.

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