MISA-web: a web server for microsatellite prediction

Beier, Sebastian; Thiel, Thomas; Münch, Thomas A.; Scholz, Uwe; Mascher, Martin

doi:10.1093/bioinformatics/btx198

Cited by 1,489 publications

(1,109 citation statements)

References 12 publications

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“…The reads with high quality score were assembled into contigs using CLC genomics workbench 10.1.1 (Qiagen, USA). Microsatellites were identified from these contigs using online Microsatellite Identification tool (MISA) (Beier, Thiel, MÜnch, Scholz, & Maascher, ). A total of 20 primer pairs were designed and screened using 30 samples of S. seenghala .…”

Section: Methodsmentioning

confidence: 99%

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Development and characterization of 15 novel polymorphic microsatellites for Giant river-catfish Sperata seenghala (Sykes, 1839) using next generation sequencing approach

et al. 2018

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Section: Methodsmentioning

confidence: 99%

“…Microsatellite Identification tool (MISA) (Beier, Thiel, MÜnch, Scholz, & Maascher, 2017). A total of 20 primer pairs were de- Taq buffer containing 1.5 mM MgCl 2 .…”

Section: Microsatellites Were Identified From These Contigs Using Onlinementioning

confidence: 99%

Development and characterization of 15 novel polymorphic microsatellites for Giant river-catfish Sperata seenghala (Sykes, 1839) using next generation sequencing approach

et al. 2018

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“…Other parameters were used as default. In addition, the compound microsatellite and imperfect microsatellites were excluded in this analysis, thus there was no different result for the microsatellite extraction while we using other extracting tools or algorithms for checking, like MfSAT [35], RepeatMasker [36] and MISA [37]. The results of these methods were not significantly different (data not shown).…”

Section: Extraction Of Microsatellitesmentioning

confidence: 97%

Conserved microsatellites may contribute to stem-loop structures in 5′, 3′ terminals of Ebolavirus genomes

Zhang

Peng

et al. 2019

Biochemical and Biophysical Research Communications

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a b s t r a c tMicrosatellites (SSRs) are ubiquitous in coding and non-coding regions of the Ebolavirus genomes. We synthetically analyzed the microsatellites in whole-genome and terminal regions of 219 Ebolavirus genomes from five species. The Ebolavirus sequences were observed with small intraspecies variations and large interspecific variations, especially in the terminal non-coding regions. Only five conserved microsatellites were detected in the complete genomes, and four of them which well base-paired to help forming conserved stem-loop structures mainly appeared in the terminal non-coding regions. These results suggest that the conserved microsatellites may be evolutionary selected to form conserved secondary structures in 5 0 , 3 0 terminals of Ebolavirus genomes. It may help to understand the biological significance of microsatellites in Ebolavirus and also other virus genomes.

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“…Potential EST-SSR loci were identified from 62,474 unigenes using the MIcroSAtellite (MISA) perl script (Beier, Thiel, Münch, Scholz, & Mascher, 2017). EST-SSR loci of repeat length at least 20 bp were used for subsequent primer design (Singh et al, 2010).…”

Section: Materials S and Me Thodsmentioning

confidence: 99%

Development of 28 EST‐SSR markers based on transcriptome sequences of Gobiobotia filifer and cross‐species amplification

et al. 2019

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Gobiobotia filifer is a small benthic fish distributed in Yangtze River Basin. The abundance of G. filifer increased after impoundment of Xiluodu Dam and Xiangjiaba Dam. The state of population structure and changes of genetic diversity before and after impoundment of Xiluodu Dam and Xiangjiaba Dam were interesting issues. However, efficient molecular markers were rare, which will limit us to solve above problems. Twenty‐eight expressed sequence tag SSRs (EST‐SSRs) were successfully identified and verified as stable amplification and polymorphic loci by polyacrylamide gel electrophoresis (PAGE) and capillary electrophoresis. The number of alleles at these EST‐SSR loci ranged from 3 to 14, the polymorphism information content values were 0.125–0.897, and the observed and expected heterozygosities were 0.0–0.857 and 0.132–0.928, respectively. Cross‐species amplification of the 28 loci developed in this study was examined in seven individuals of each of the 7 taxa. The amplification efficiency of 28 EST‐SSRs primer pairs is related to the distance of genetic relationship between cross‐species with G. filifer, and same subfamily species (Xenophysogobio boulengeri and Xenophysogobio nudicorpa) showed the highest (50%) amplification efficiency. These EST‐SSR markers could be used to analyse genetic diversity and population structure of G. filifer and related species.

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MISA-web: a web server for microsatellite prediction

Cited by 1,489 publications

References 12 publications

Development and characterization of 15 novel polymorphic microsatellites for Giant river-catfish Sperata seenghala (Sykes, 1839) using next generation sequencing approach

Development and characterization of 15 novel polymorphic microsatellites for Giant river-catfish Sperata seenghala (Sykes, 1839) using next generation sequencing approach

Conserved microsatellites may contribute to stem-loop structures in 5′, 3′ terminals of Ebolavirus genomes

Development of 28 EST‐SSR markers based on transcriptome sequences of Gobiobotia filifer and cross‐species amplification

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