Sentence examples for parameters were aligned from inspiring English sources

Individual pathway modules were then integrated wherein kinetic parameters were aligned wherever necessary by following the optimization method described above.

Contigs were aligned with alignment parameters set to > 97% identity and > 40 nucleotides overlap using Sequencher (Gene Codes Corp., Ann Arbor, MI, USA).

Using Cufflinks (Trapnell et al., 2010) with default parameters, B. schlosseri cDNA reads were aligned to the draft assembly and a reference-guided transcript assembly was produced.

All sequences were aligned with default BLAST alignment parameters to the UCD10X v1.0 pseudomolecules to identify the PUN1 sequence.

Reads were aligned using default parameters allowing up to 40 alignments per read with a maximum 2-bp mismatch.

Protein sequences were aligned with default parameters in CLUSTALW (http://align.genome.jp/) and outputted as alignments using the BOXSHADE package (http://www.ch.embnet.org/software/BOX_form.html).html

The OrthoMCL program [ 62] was used to cluster SEO proteins into subgroups, with an inflation parameter of 3. The protein sequences were aligned with T-Coffee [ 63] and the alignment was end trimmed to start and end with the domains predicted for all SEO proteins (SEO-NTD and SEO-CTD).

The sequences were aligned using default parameters [29].

Sequences were aligned using default parameters in MUSCLE v3.8.31 (Edgar 2004).

Sequences were aligned using default parameters of CLUSTALX v.2 [ 48] and further inspected by eye to maximize positional homology.

Sequences were aligned using default parameters in MAFFT [ 95], except for COI, which was aligned using MAFFT(−einsi) for improved accuracy.