The default is to perform a simple exact-string match.
We used default parameters to perform the analyses and accepted the CPC pre-defined decision scores.
We used the "rma" function with default settings to perform background correction and normalization.
The options were set as default, except to perform three iterations with the E-value threshold for inclusion at 0.001.
Eland II (from Illumina pipeline version 1.6) was used with the default parameters to perform sequence alignment to the 300-bp synthetic DNA construct.
Several parameters can be customized to tailor the analysis, even if optimal default parameters to perform a standard workflow are suggested.
For ensuring high-quality data, we used NGS QC Toolkit with default parameters to perform quality control of raw sequencing data, mainly by removing low-quality reads and reads containing primer/adaptor contamination [ 60].
RLSB, as a regulator of rbcL gene expression, provides a new insight into how one component of this extensive photosynthetic regulatory system might have been modified from an original C3 "default" function to perform the same function, but in a more specialized fashion, in C4 plants.
The blastall executable by default uses BLOSUM62 to perform alignments of amino acid sequences, and this is the matrix used in all stages before composition adjustment is performed.
For this work, the annotations of W. ceti WS08, WS74 and WS105 were updated in Prokka version 1.10, with default parameters, changing to perform BlastP similarity searches in nested databases, on this order: TrEMBL Uniprot containing only Weissella spp. proteins, RefSeq database containing only Weissella spp. proteins, and complete RefSeq database.
Stretching to the corners with your thumb is darn near impossible and to complete even simple actions like closing a modal view inside an app it's often easiest (and most habitual) to just default to two hands to perform those actions.
