Sentence examples for alignment of clusters from inspiring English sources

The clusters with no hits in the TrED EST sequences and NR were used for the following steps: (1) alignment to non-coding RNA sequences with rRNA sequences downloaded from Rfam and GenBank [ 40], (2) identification of tRNAs with tRNAscan-SE (version 1.1) [ 41], and (3) alignment of clusters to Rfam sequences using HMMER (version 3.0) [ 42] and INFERNAL (version 1.0.2).

The sequence alignment of Cluster IV toxins is shown in supplementary figure S3 (Supplementary Material online).

We built PSI-BLAST profiles (position-specific substitution matrix) for each cluster, using the alignment of cluster members as an input against NR database at an Evalue = 10-10.

The same software (MUSCLE and FastTree) was used to reconstruct approximate maximum likelihood (ML) phylogenetic trees from multiple alignments of Clusters of Orthologous Group COGG) representatives that were used for Xenologous Gene Displacement (XGD) detection.

Quality filtered CCS sequences were clustered based on a 98% similarity threshold with the -cluster_fast option and resulting alignments of clusters containing ≥ 7 sequences (i.e., a 7× threshold) were imported into the Geneious software package (v6.1; http://www.geneious.com) re-aligned using the MAFFT (v7.017) alignment plugin and then manually edited for accuracy.

MCL was run by setting the inflation parameter (I equal to 4. The alignments of clustered elements were produced by PCMA [ 20] used with default parameters.

Alignments of clustered MITE sequences were examined manually, and 66 of these were discarded due to poor overall similarity or due to extensive similarity in the sequences flanking the inverted repeats, indicative of the inverted repeat being within a larger repeat element.

From our previous work, we concluded that the mechanism of magnetic wires proceeds in two steps: (i) the formation and growth of spherical clusters of particles and (ii) the alignment of the clusters induced by the magnetic dipolar interactions [51].

It can be concluded that the vorticity alignment of GO clusters induces the negative ΔN based on the optical shear experiments.

From the alignment of all clusters from the same fraction to the midpoint, we can assess the general conservation level of the small RNAs and their surroundings, here expressed as the mean PhastCons score.

GeMMA exploits COMPASS (Sadreyev and Grishin, 2003) to compare the profiles derived from the multiple sequence alignments (MSAs) of clusters present at each stage of the clustering.