Sentence examples for motifs were aligned from inspiring English sources

Secondary structure elements and Hanks and Hunter subdomain motifs were aligned manually.

The sequences containing repetitive motifs were aligned among accessions to reveal variation among individuals.

For illustration, c. 110 bp of sequence flanking the putative helitron motifs were aligned using ClustalW with manual adjustment in GenDoc.

RSI motifs were aligned using WebLogo (Supporting Information Figure S14-A), and it was seen that three Glu and three Leu residues were the most conserved.

To test if the presence of discovered motifs in eRNAs was associated with some larger (hence, more general) primary RNA structures, the 32 RNAs containing all 3 motifs were aligned using Clustal.

Coordinates for three TRBV bearing the CASG motif and seven with the CASS motif were aligned to define the molecular consequences of this G/S variation.

Multiple occurrences of each motif were aligned and submitted to Weblogo [ 73].

The deduced amino acid sequences of the conserved HK domain, Rec domain, Hpt domain, Myb domain, and CCT motif were aligned using the ClustalX program.

Next, sequences of all the proteins identified by the InterProScan as containing an EF-hand motif were aligned using Clustal X [ 16] [see Additional file 2].

Sequences similar to Cox17p, Cox19p, Mrp10, CHCHD7, and uORF homology group 8 (as determined by tBLASTn and analyzed for conservation of the CHCH motif) were aligned using Muscle [ 85], trimmed of non-informative sites, and analyzed using Mr. Bayes v. 3.0 [ 86] (rates = gamma, aamodel = mixed, ngen = 2000000).

The structural model of the HpyAV ββα-Me motif was aligned pair-wise with the crystal structures of ColE9 (PDB: 1V14), I-HmuI (PDB: 1U3E), Hpy99I (PDB: 3GOX) and the KpnI model built by Nagaraja and colleagues [36] using the TM-Align module [78] of STRAP [79].