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This approach therefore appears to be a promising strategy for improving the development of microsatellites, as it introduces no major bias in terms of the proportions and distribution of microsatellites.
However, we used this set of parameters in the application of this methodology to the isolation of microsatellites as it led to the rapid and efficient development of 105 microsatellite loci in Zingel asper (Linnaeus, 1758) [Actinopterygii: Perciformes: Percidae] (see Additional file 1, Table S2).
This was apparently not due to a failure of the program to detect microsatellites, as it recovered 429 such microsatellites when run with the D. pseudoobscura bogotana GSS sequences, despite there being 25% fewer sequence reads than in the M. scalaris GSS.
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This tool allowed for the identification and localization of perfect microsatellites as well as compound microsatellites.
This tool allowed the identification and localization of perfect microsatellites as well as compound microsatellites.
The longest SSRs were genomic microsatellites (as long as 726 bp).
Mononucleotide repeats (with a repeat length of 6 nt) were identified using the tool IMEX (Imperfect Microsatellite Extractor), which can extract perfect microsatellites as well as imperfect microsatellites.
For M. bechsteinii, individuals from ten maternity colonies had been genotyped for eight nucDNA microsatellites as well as two mitochondrial microsatellites [ 20, 32].
The detailed polymorphic loci of each of these microsatellites as well as their frequencies are reported in Table 2.
We find mutations in homopolymeric runs as small as four nucleotides and mutations in microsatellites as small as three repeat units, or six nucleotides.
Software tools exist [ 37, 38] and databases such as MICdb store predicted microsatellites as well as offering a prediction tool for user inputted sequence [ 39].
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