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Spotfinder specifications


Unique identifier OMICS_29427
Name Spotfinder
Alternative name TIGR_Spotfinder
Software type Toolkit/Suite
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C++
License Artistic License version 2.0
Computer skills Medium
Stability Stable
Maintained Yes




No version available

Additional information

Spotfinder citations


Mutual independence of alkaline‐ and calcium‐mediated signalling in Aspergillus fumigatus refutes the existence of a conserved druggable signalling nexus

Mol Microbiol
PMCID: 5725717
PMID: 28922497
DOI: 10.1111/mmi.13840
call_split See protocol

[…] The RNA samples were shipped to the microarray facility at the J. Craig Venter Institute (Rockville, MD) for further analysis using the standardized facility protocols available at Briefly, 30 μg of total RNA was mixed with 20 μg of Random Primer Hexamers (GE Healthcare), 100 pmol of oligo dT (Invitrogen) and 40 U of RNAseOUT (Invitrogen) in a volume of 13 μl an […]


Proteomic composition of the acrostyle: Novel approaches to identify cuticular proteins involved in virus–insect interactions

PMCID: 5724696
PMID: 28421675
DOI: 10.1111/1744-7917.12469

[…] dia, Elkhart, IN, USA) and anti‐P2 (Blanc et al., ) primary antisera, and GAR‐AP secondary antiserum as described above. Hybridizations on the peptide array were quantified using standard conditions (Spotfinder v3.2.1; available online at The intensities of replicate spots were averaged, and considered positive when >8000 units. This threshold, defined arbitrar […]


Enhanced control of Mycobacterium tuberculosis extrapulmonary dissemination in mice by an arabinomannan protein conjugate vaccine

PLoS Pathog
PMCID: 5360349
PMID: 28278283
DOI: 10.1371/journal.ppat.1006250
call_split See protocol

[…] ned and analyzed as described previously []. Briefly, slides were scanned on a GenePix 4000A scanner (Molecular Devices, Sunnyvale, CA) and processed with the TM4 software suite ( TIGR Spotfinder was used to grid and quantify spots. TIGR MIDAS was used for Lowess normalization, standard deviation regularization and in-slide replicate analysis, with all quality control flags on […]


Dual Reporter Mycobacteriophages (Φ2DRMs) Reveal Preexisting Mycobacterium tuberculosis Persistent Cells in Human Sputum

PMCID: 5080378
PMID: 27795387
DOI: 10.1128/mBio.01023-16
call_split See protocol

[…] Slides were rinsed with MilliQ water followed by drying by centrifugation for 1 min at 1000 rpm. Slides were scanned on a GenePix 4000A scanner and images were processed with the TM4 software suite. TIGR Spotfinder was used to grid and quantitate spots, and TIGR MIDAS was used for Lowess normalization, standard deviation regularization, and in-slide replicate analysis. The results were analyzed i […]


On the role of ethylene, auxin and a GOLVEN like peptide hormone in the regulation of peach ripening

BMC Plant Biol
PMCID: 4750175
PMID: 26863869
DOI: 10.1186/s12870-016-0730-7
call_split See protocol

[…] ely hybridized to oligonucleotide microarrays platform μPEACH1 (GEO ID: GPL8584). Microarrays were read with the ScanArray LITE confocal laser scanner (PerkinElmer, USA) and the values extracted with Spotfinder 3.1 [] as previously described [].Normalized data were loaded in MeV 3.1 [] and subjected to SAM (Significance Analysis of Microarrays, [] analyses. Since the comparison (Class 0 36 h air → […]


Analysis of the Salmonella regulatory network suggests involvement of SsrB and H NS in σE regulated SPI 2 gene expression

Front Microbiol
PMCID: 4322710
PMID: 25713562
DOI: 10.3389/fmicb.2015.00027

[…] xpressed genes.First, we calculated a single, background-corrected intensity for the probes (spots) on each of our arrays. Using the scanned array image, we quantified the probe intensities using the Spotfinder tool from the TM4 Microarray Software Suite (Saeed et al., , ), giving us an MEV file for each array. To load and manipulate the intensity data in the MEV files, we used Bioconductor's limm […]


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