Sentence examples for reduced alignments from inspiring English sources

We also ran INTREPID on these reduced alignments as well as the full alignments for these 71 families.

We systematically removed the fastest evolving sites one at a time, and rebuilt ML phylogenies based on these reduced alignments.

Reduced alignments containing sets of representative sequences of less than 90% identity were obtained by using the CD-HIT suite [ 66].

Gblocks version 0.91 b (Castresana 2000) was used to remove poorly aligned regions from each alignment, and the reduced alignments were concatenated using Gblocks with options "-t = c -a = y -c = y -w = y".

The reduced alignments were then treated as separate profiles and re-aligned using MUSCLE [ 40].

Identical cox1 haplotypes and PEPCK genotypes were then removed from the alignments using Collapse 1.2 [54], with heterozygote and unknown bases considered as different characters from homozygous sites, resulting in final reduced alignments of 161 cox1 haplotypes and 179 PEPCK genotypes (Table 2).

Reduced alignment and increased entanglement are the reasons of this decrease.

We found that knockout of syndecan-1 reduced alignment of vascular smooth muscle cells to the nanogrooves under inflammatory treatments.

Phylobayes analyses with the CAT model were also done on each reduced alignment.

Wound treatment with C15, however, resulted in collagen deposition with a more random collagen fiber orientation closer to unwounded dermal collagen organization, which equated to reduced alignment in comparison to that of vehicle-treated wounded skin (C15: 0.71 ± 0.02; Figures 4A 4C).

We also reduced alignment error by finding cases where the 3' splice site of a candidate SJ (retrieved directly from RNA-Seq alignments) was located within 6 bp of 5' end of a read or the 5' splice site of a candidate SJ was located within 6 bp of 3' end of a read.