SPUTNIK statistics

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Citations per year

Number of citations per year for the bioinformatics software tool SPUTNIK
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Tool usage distribution map

This map represents all the scientific publications referring to SPUTNIK per scientific context
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SPUTNIK specifications

Information


Unique identifier OMICS_30765
Name SPUTNIK
Alternative name SPatially aUTomatic deNoising for Ims toolKit
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU Lesser General Public License version 3.0
Computer skills Advanced
Version 1.0.3.4
Stability Stable
Requirements
methods, ggplot2, reshape, viridis, infotheo, R(≥3.4.0), SDMTools, spatstat, autothresholdr, imager
Maintained Yes

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Versioning


No version available

Maintainer


  • person_outline Paolo Inglese

Publication for SPatially aUTomatic deNoising for Ims toolKit

SPUTNIK citations

 (4)
library_books

Deep landscape update of dispersed and tandem repeats in the genome model of the red jungle fowl, Gallus gallus, using a series of de novo investigating tools

2016
BMC Genomics
PMCID: 4992247
PMID: 27542599
DOI: 10.1186/s12864-016-3015-5

[…] model has been estimated, using RM, to be 1.73 % []. We reinvestigated this number by examining the diversity and number of microsatellites using the FASTA program of the GCG computer package [] and sputnik [] while those of satellite DNAs were investigated using a variety of molecular approaches (for a review see []). Using TRF, which can detect SSRs with repeated units from 1 bp to 2 kbp, we fo […]

library_books

Allelic variation at the rpv1 locus controls partial resistance to Plum pox virus infection in Arabidopsis thaliana

2015
BMC Plant Biol
PMCID: 4479089
PMID: 26109391
DOI: 10.1186/s12870-015-0559-5

[…] hanically inoculated PPV in Cvi-1, a total of twenty molecular markers were developed (see Additional file : Table S3). Microsatellite repeat motifs were identified in Arabidopsis BAC sequences using Sputnik software (http://www.appliedbioinformatics.com.au/projects/ssrPrimer/cgi-bin/index). Simple sequence length polymorphism (SSLP) and Single Nucleotide Polymorphism (SNP) were retrieved from the […]

library_books

STAMP: Extensions to the STADEN sequence analysis package for high throughput interactive microsatellite marker design

2009
BMC Bioinformatics
PMCID: 2644677
PMID: 19183437
DOI: 10.1186/1471-2105-10-41

[…] llites are well suited and should thus be correctly recognized in a modern MS design workflow. Of the existing MS marker design pipelines cited above, only SSR PRIMER (using the repeat detection tool SPUTNIK), MSATFINDER (using SPUTNIK or an algorithm designed by the authors) and SAT (also using SPUTNIK) can detect imperfect repeats, however only with a limited accuracy. Finally, even if primers s […]

library_books

Comparative BAC end sequence analysis of tomato and potato reveals overrepresentation of specific gene families in potato

2008
BMC Plant Biol
PMCID: 2324086
PMID: 18405374
DOI: 10.1186/1471-2229-8-34

[…] Microsatellites were detected using a modified version of the Sputnik software []. Running parameters were set to return all SSRs spanning at least 15 nucleotides, with a motif length between 1 and 5 (i.e., mono-, di-, tri-, tetra-, and penta-nucleotide repeats) […]


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SPUTNIK institution(s)
Computational and System Medicine, Department of Surgery and Cancer, London, UK
SPUTNIK funding source(s)
Supported by Cancer Research UK Grand Challenge Program and the National Institute for Health Research (NIHR) Imperial Biomedical Research Centre (BRC).

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