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Filtered reads were aligned to respective genomes allowing 2 mismatches and only uniquely aligning reads were considered.
The simulated SSU and LSU ribo-tags from the test species were then aligned to respective filtered database versions using BLASTN and taxonomically assigned using MEGAN, as described above.
Resulting amino acid sequences were aligned to respective sequences from the WSSV-CH or WSSV-TH genomes in MAFFT v. 7.017 (G-INS-i mode) [ 27].
Reads were trimmed for low-quality positions and then aligned to respective genome assemblies using STAR v2.4.0 (Dobin et al. 2013) with gene annotations as guidance (supplementary table S9, Supplementary Material online).
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The OBPs and the D7 sequences were aligned to their respective structure alignments as profiles, and a combined alignment of the two family of proteins was constructed using the profile profile alignment option using ClustalX (Thompson et al. 1994, 1997; Jeanmougin et al. 1998).
Reads were aligned to their respective genomes using the MOSAIK alignment program allowing for a threshold of two mismatches between each 35 base pair read and the reference genome.
We find evidence for this inadequacy by comparing the alignment summary statistics for B6 and CAST liver samples aligned to their respective strain-specific transcriptomes.
Over 156 million single end AB SOLiD reads aligned to their respective genomes (54%) using the MOSAIK alignment program (http://bioinformatics.bc.edu/marthlab/Mosaik) as described in Methods and Additional File 1, Supplemental Methods 1.
The assembled contigs were thereafter aligned to their respective gap position to precisely identify the added sequences.
The Dikpalas and their consorts are seen with their mounts and aligned to their respective directions.
The individual PET images were spatially aligned to their respective MRI images using 3D voxel registration with a linear transformation (Analyze 8.1, Mayo Clinic).
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CEO of Professional Science Editing for Scientists @ prosciediting.com