Sentence examples for alignment the parameters from inspiring English sources

As for the raw RNA-Seq read alignment, the parameters of TopHat2 are set as follows: min − anchor − length = 4, min − intron − length = 40, max − intron − length = 2000, min − segment − intron = 40, max − segment − intron = 2000, min − coverage − intron = 40, and max − coverage − intron = 2000.

In order to assess topological support, 500 bootstrap replicates were performed with RAxML on each alignment with the parameters described above.

Hence, the more stringent the alignment parameters, the fewer usable transcripts that are obtained, leading to a decrease in performance of L_RNA_scaffolder.

To give the best alignment, the alignment parameter Constraint E-value and Word Size were adjusted for different datasets when using COBALT.

After several cycles of 3D classification and refinement, a 2D classification step using the alignment parameters from the 3D refinement was performed to check the alignment accuracy and to further exclude particles liable to misalignment.

The method was modified for recombinant sequences by allowing the genealogy to vary across the alignment while sharing the parameters of the codon substitution model between tracts [56].

G Comparison between 30S subunit of the 70S ribosome 3D reconstructed from dataset fraction #1 (blue) and fraction #2 (purple) using the alignment parameters from the 3D auto-refinement of segmented 50S subunit.

The alignment parameters were the following: -a –b –D –o -2 –u –m –x (-g) –l 32 –s 30 –v 3. Duplicated reads caused by PCR were removed using an in-house C++ script.

After finding the alignment parameters for these resolutions, we use the alignment to register the facial images using an interocular distance of 50 pixels.

In addition, changing the alignment parameters (such as the Gap penalty) or specifying certain assumptions (such as the presence of low complexity sequences interrupting a conserved domain) are likely to give different results.

However, RScan could detect more alignments when tuning the parameters.