Sentence examples for by aligning the sequences from inspiring English sources
A MSA of the H. irregulare GH61 sequences was obtained by aligning the sequences to a profile consisting of a 3D-structural alignment of TtGH61E and HiGH61B from Thielavia terrestris; PDB ID: 3EII (Harris et al. 2010) and Hypocrea jecorina; PDB ID: 2VTC (Karkehabadi et al. 2008), respectively (Figs. 1 and 2).
TaqMan® probes and primers specific for the BDV P and BDV L genes were designed by aligning the sequences of known BDV strains.
For the KIBA dataset we downloaded the protein sequences from NCBI and computed the normalized Smith Waterman similarity for each pair by aligning the sequences using the Biostrings R package.
A secondary structure for each input sequence is predicted via RNAfold and a consensus structure is obtained by aligning the sequences using alifold [11].
We further analyzed the MIC17 proteins from both Neospora and Toxoplasma by aligning the sequences, assessing sorting signals, and conducting protein domain searches (Figure S1).
Conventional sequences were assembled and edited in Seqscape v2.5 (Applied Biosystems, USA) with sequence variations identified by aligning the sequences with HXB-2 (Accession number: K03455).
The transposon insertion site was determined by aligning the sequence to the F. tularensis SCHU strain genome database (www.Francisella.org).
SNP calling was performed by aligning the sequence reads from each individual to the assembled contigs with Novoalign (version 2.07) [10].
Furthermore, by aligning the sequence reads to the E. coli strain W3110, we screened sequence differences between two E. coli strains using data sets of three different next-generation platforms.
