Sentence examples for matrix and default from inspiring English sources

The corresponding scaffold residues of the target and template sequences are then 'anchored' and pairwise sequence fragments between subsequent anchors are aligned using standard functions from the MATLAB bioinformatics toolbox with the BLOSUM62 scoring matrix and default gap penalties.

The alignments were constructed with ClustalW option of MEGA, with Gonnet matrix and default parameter values.

Sequence alignment was performed with BLAST [ 43] using the BLOSUM62 scoring matrix and default parameters.

Global protein sequence alignment was performed with ClustalW (version 1.83) [ 74] using the default BLOSUM matrix and default parameters.

Multiple alignments were constructed by CLUSTAL-W using the Gonnet weight matrix and default gap penalties [ 89].

Protein sequences were aligned with ClustalW with using the Gonnet series weight matrix and default parameters http://workbench.sdsc.edu[ 56].

Multiple alignments of protein and cDNA sequences were generated with ClustalW.1.83 using Gonnet/IUB matrices and default parameters [ 99].

The final set of homologues were aligned using CLUSTALW 38 program using BLOSUM matrix and the default parameters.

The PSI-BLAST searches were run for a maximum of 20 iterations using a BLOSUM62 transition weight matrix and the default gap opening and extension penalties of 11 and 1, respectively.

For this analysis we used a 4 × 3 matrix and the default settings of the software (random vectors method of initialization, bubble neighborhood definition, αi = 0.1, σi = 5, αf = 0.005, σf = 0.5).

The parameter is used to make sure that the positive definiteness of the covariance matrices and the default choice of should work for most of the cases.