SciRoKo protocols

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SciRoKo specifications

Information


Unique identifier OMICS_00113
Name SciRoKo
Alternative name SSR Classification and Investigation by Robert Kofler
Software type Package/Module
Interface Graphical user interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages C#
License Mozilla Public License version 2.0
Computer skills Medium
Version 3.4
Stability Stable
Maintained Yes

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  • person_outline Robert Kofler <>

Publication for SSR Classification and Investigation by Robert Kofler

SciRoKo in pipelines

 (13)
2018
PMCID: 5883146
PMID: 29643862
DOI: 10.3389/fpls.2018.00401

[…] linking genetic resources, genomes and phenotypes of solanaceous crops)., http://faostat3.fao.org/ , www.eggplantgenome.org , www.eggplantmicrosatellite.org/ , http://kofler.or.at/bioinformatics/sciroko , http://bedtools.readthedocs.io , http://systemsbiology.cau.edu.cn/agrigov2/ , revigo.irb.hr/ , https://sourceforge.net/projects/primer3 , www.artichokegenome.unito.it/cymsatdb/ , […]

2017
PMCID: 5603166
PMID: 28922359
DOI: 10.1371/journal.pone.0184319

[…] sequence tag (est) database of 23,845 cdna sequences was downloaded and assembled using cap3 software [] with default settings. the resulting contig and remaining singlet sequences were mined with sciroko software [] for di-, tri- and tetranucleotide repeat sequences with a minimum of 10 nucleotides. ssrs meeting this criteria were selected for the presence of ≤300 bp flanking sequences […]

2016
PMCID: 4824173
PMID: 26868597
DOI: 10.1093/gbe/evw019

[…] significantly enriched in the dataset at padj < 0.05. as an additional metric of comparison across clade b species, we mined all transcriptomes for repeats and flanking regions using the software sciroko () and considered repeat motifs between 2 and 6 bp., to test for differential expression between the four species, it was necessary to identify a set of comparable orthologous genes. open […]

2016
PMCID: 4845337
PMID: 27112435
DOI: 10.1186/s13104-016-2039-x

[…] using the trinity genome-independent transcriptome assembler [release 17 july 2014, ] with a minimum transcript length of 300 bases (for further details see []). transcripts were screened using sciroko v. 3.4 []. di-, tri-, tetra-, penta-, hexa-, hepta-, octa-, nona-, and deca-nucleotide repeat motifs were searched, setting the minimum repeat units to five, for all motif categories. among […]

2016
PMCID: 5077286
PMID: 27785387
DOI: 10.3732/apps.1600072

[…] fraction of 0.4, similarity fraction of 0.4, insertion cost of 2, deletion cost of 2, and a minimum contig length of 200 nucleotides. we extracted the contigs containing microsatellite markers with sciroko version 3.1 (), using default identification criteria used for mono-, di-, tri-, tetra-, penta-, and hexanucleotide repeats, with a minimum of 14, seven, five, four, four, and four repeats, […]


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SciRoKo in publications

 (61)
PMCID: 5883146
PMID: 29643862
DOI: 10.3389/fpls.2018.00401

[…] downloaded in fasta format. its 12 pseudomolecules (representing partial sequences of each of the species’ chromosomes), along with all unmapped scaffolds, were chopped into manageable pieces using sciroko tool. perfect, compound, and imperfect ssrs were identified in silico using the sciroko ssr—search module (see footnote 4). a minimum of four repetitions together with a minimum length of 15 […]

PMCID: 5870257
PMID: 29580224
DOI: 10.1186/s12864-018-4610-4

[…] identified by ltrharvest [] and ltrdigest []. all detected classified tes were soft-masked by repeatmasker v.4.0.6 (http://www.repeatmasker.org/) (additional file : method)., ssrs were scanned by sciroko v.3.4 [] with perfect misa-mode (default setting). ssr motifs were standardized by grouping motifs in different reading frames and corresponding reverse complements together. the distribution […]

PMCID: 5857172
PMID: 29576965
DOI: 10.7717/peerj.4495

[…] in imperfect microsatellites is still very limited and their correlation with life history traits remains to be revealed and explained., in this study, we used 65 avian genome sequences, employing sciroko () to search ssrs in the whole genome. we chose avian genomes for this study because microsatellites have been widely used in population genetics of bird species, yet the pattern […]

PMCID: 5674736
PMID: 29110701
DOI: 10.1186/s12864-017-4234-0

[…] file : table s1). the genome sequences of all insects were downloaded from insectbase 1.0 []. ambiguous nucleotides were removed from the genomes prior to analysis., ssrs were identified using the sciroko 3.4 using default parameters []. according to the motifs, the repeat sequences were divided into six classes: mono-, di-, tri-, tetra-, penta-, and hexa-nucleotide ssrs []. for each class, […]

PMCID: 5437633
PMID: 28529469
DOI: 10.1186/s41065-017-0034-4

[…] were obtained from ncbi genome portal []. the name of each species was abbreviated to four letters where first capital letter denoted to genus and trailing three letters as species name., the sciroko (v3.4) program utility [] was used with default imperfect search parameters to identify imperfect microsatellites of varying motif length from 1 to 6 nucleotide (nt) that were designated […]


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SciRoKo institution(s)
University of Natural Resources and Applied Life Sciences, Department for Agrobiotechnology IFA-Tulln, Institute of Biotechnology in Plant Production, Tulln, Austria; Institut für Ökologie, Universität Innsbruck, Innsbruck, Austria; Institut für Tierzucht and Genetik, Veterinärmedizinische Universitat Wien, Wien, Austria
SciRoKo funding source(s)
The Austrian Science Fund (FWF, No P18414-B14); the Fonds zur Förderung der wissenschaftlichen Forschung (FWF)

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