SciRoKo protocols

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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Maintainer


  • person_outline Robert Kofler <>

Publication for SSR Classification and Investigation by Robert Kofler

SciRoKo IN pipelines

 (6)
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 [42] with default settings. the resulting contig and remaining singlet sequences were mined with sciroko software [43] 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 […]

2015
PMCID: 4535569
PMID: 26163593
DOI: 10.1093/jisesa/iev069

[…]  < 20, homopolymer stretches ≥ 6 nt, and minimum length = 100 using the script 454qc.pl from the ngsqctoolkit (patel and jain 2012). the resulting filtered reads were used as input for the program sciroko (koefler et al. 2007) that identified mismatched microsatellite di-, tri-, tetra-, and pentanucleotide repeat motifs > 3 units in length, and a base substitution mismatch penalty of 5, seed […]

2013
PMCID: 3878662
PMID: 24341590
DOI: 10.1186/1471-2164-14-883

[…] to total contigs., ssrs are potential genetic markers due to their high rate of polymorphisms. to investigate the ssr contents and their distribution in uv-8b bess, we scanned the bes dataset with sciroko3.4 [24]. first, the cap3 [25] program was used to reduce the redundancy of bess; it clustered 1,821 bess into 803 contigs and left 4,739 reads as singletons. the total length of these reads […]

2013
PMCID: 3878662
PMID: 24341590
DOI: 10.1186/1471-2164-14-883

[…] and distribution patterns, the gss sequences of b. graminis, fusarium virguliforme, m. oryzae and t. reesei were downloaded from ncbi and scanned for ssrs using the same parameters of cap3 and sciroko programs. the ssr contents and distribution patterns varied obviously (figure 5). the ssr densities of the above species were 96.27/mb, 107.71/mb, 173.60/mb and 234.06/mb, respectively, […]

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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