Sentence examples for backbone alignment from inspiring English sources

First, the HTS reads are aligned to a backbone alignment [ 71, 72], subsequently each query sequence is placed into a backbone tree [ 73] using an extended alignment, and finally taxonomy is assigned to each read using a phylogenetic placement approach, such as the Lowest Common Ancestor (LCA) [ 74].

The resulting sequences were aligned in ARB (Ludwig et al. 2004) to a backbone alignment from the Greengenes 16S rRNA database (http://greengenes.lbl.gov) (DeSantis et al. 2006).

Performing a peptide backbone alignment revealed that the 3D-structure of the peptide backbone was highly conserved [44].

After performing a backbone alignment of the peptides, it was determined that the three peptides have a similar binding conformation.

Next, a peptide backbone alignment was performed on the three co-binding peptides present in addition to superimposition of bound abacavir from the three crystals.

When using P1 (from 3VRI) as a reference, the backbone alignment has been measured with an RMSD of 1.23 and 1.78 Å with P2 (3VRJ) and P3 (3UPrespectivelyely, as shown in Fig. 4.

All sequence-based backbone alignments were preformed using the molecular graphics program, Friend [74] and structure-based alignments were achieved with the Calpha-based algorithm, Topofit [75], also present in Friend.

Because these are strongly affected by the environment, the trade-off among these fragment-interactions and the key nucleation sites may determine the polymorphic oligomer (and fibril) outcome, particularly with respect to parallel/antiparallel backbone alignments.

The cDNA sequence reads from RNA-seq were trimmed to remove Illumina sequencing adaptors as well as unreliable read ends, and alignments were performed using the CEN.PK113-7D CEN.PK113-7Dnce and associated genomele [ 77] asequenceckbone for andgnment massociated quantitation.

The backbone Cα alignment of MRG701CD, MRG2CD, and MRG15CD showed that the backbone Cα of MRG701CD matches the backbone Cα of MRG2CD and MRG15CD quite well, with r.m.s.d. of 0.461 and 0.690 Å, respectively (Fig. 2D).

The backbone structural alignment of UT4 with 3BEV and 3P73 [ 49], the top 2 structural analogs for UT4 and UT8, are shown in Fig.  5b.