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To map the simulated time to wet-lab time, we relied on the finding that AT II cells in 2% Matrigel cultures migrate ∼1.7 µm in 15 minutes [6].
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Table 1 shows that, in addition to increasing marker density, integrating more linkage maps tends to reduce the error between the consensus map and the simulated physical map.
Malynda Chizek, an astronomy graduate student at New Mexico State University, recently outlined her research results on mapping the simulated methane distribution during different seasons on Mars.
We mapped the simulated paired-end reads onto the consensus using Mosaik.
To identify these specific regions, we mapped the simulated exome sequencing reads to either both genomes together or to only the C57BL/6 J genome.
To determine if there were differences in the observed bias among three popular mapping algorithms, we mapped the simulated 35 bp reads to the SNP-masked genome using each mapping program [MAQ v. 0.7.1, as used for the analyses of the real data in this article (Li et al., 2008); BOWTIE v. 0.9.9.2 (Langmead et al., 2009); and BWA v. 0.4.6 (Li and Durbin, 2009)].
The resolutions of both the EM map and the simulated electron density map were 21 Å.
The robustness of the map was tested by comparison of the likelihood of the reference map to the likelihood of maps derived from the reference map by all possible permutations in a window of 6 markers and by inversion of parts of the map using the simulated annealing algorithm.
The simulations were performed with molecules placed in vacuum, monitored by the global correlation coefficients between the density map and the simulated model.
At both sides, the antennas are placed at an height of 1 m. Figure 4 shows a 2-D map of the simulated environment as well as the positions of the receivers and sources.
For paired-end mapping of the simulated data, we used Burrows-Wheeler Aligner (BWA) [ 20] with the default options.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com