Sentence examples for multiple alignments including from inspiring English sources
For each MITE group, multiple alignments (including gapped positions) were created from which similarity matrices were calculated using BioEdit software, version 7.0.5.3 (http://www.mbio.ncsu.edu/BioEdit/bioedit.html).html
Simulation studies show that the trimmed datasets returned by BMGE lead to inference of accurate trees, in particular when in presence of multiple alignments including distantly-related sequences.
To examine whether gene conversion had occurred outside the coding region, we re-examined multiple alignments including 3'-UTRs using SIMPLOT.
Finally, we obtained 1,391 sets of multiple alignments including cephalopods and other molluscs, and dN/dS values of the camera eye-specific genes.
For each such cluster, multiple alignments including only one paralog at a time were constructed using Clustal Omega (Sievers et al. 2011) and trimmed using Aliscore and Alicut (Kück 2009; Misof and Misof 2009).
A sequence obtained from such multiple alignments included all exons from individual sequences, and was considered to represent the whole gene sequence.
To align conserved motifs identified within Latimeria T2Rs, V1Rs, tetrapod T2Rs, V1Rs, teleost T2Rs and V1Rs, a multiple alignment including all six gene families was analysed.
A multiple alignment including the mouse duplicate genes, their closest paralogs, and their Inparalogs clusters (orthologs) was obtained by Tcoffee [ 54].
The selected representative sequences are indicated in the phylogeny in red in Additional file 2. The final multiple alignment including 113 sequences is shown in Additional file 5. Phylogenetic reconstruction was done using the maximum likelihood method (implemented in PHYML version 2.4.4) and the maximum parsimony method (implemented in PHYLIP version 3.65).
PSI-BLAST searches failed to identify reliable similarity of COG2929 proteins to any characterized proteins; however, the multiple alignment includes several conserved positions occupied by polar residues which is compatible with an enzymatic activity of the COG2929 family proteins.
From multiple protein alignments including sequences identified in the four aerobic bacteria (A.
