Sentence examples for matrix with gap from inspiring English sources

The alignments were based on BLOSUM62 matrix with gap opening and gap extension penalties -5 and -2 respectively.

SSEARCH was run using the BLOSUM50 matrix with gap open and extension penalties of -3 and -1, respectively.

Multiple sequence alignments were constructed using CLUSTALW algorithm using the BLOSUM series of similarity matrix with gap opening and extension penalties of 10 and 0.1 respectively.

The alignments obtained with the Gonnet 250 matrix with gap opening and extension value of 1 and default value for the other parameters were chosen on the basis of both the scores calculated and "eye" inspection of the alignments.

The non-redundant database of protein sequences (National center for Biotechnology Information, NIH, Bethesda) were retrieved using the PHI-BLAST [ 30] search tool using BLOSOM 62 matrix with gap penalities (Existence – 11 and Extension – 1) with a threshold value of 0.005 and optimal limit for cyanobacteria.

The alignment is performed by assigning scores for aligned characters in the form of a similarity matrix, with gaps being heavily penalised.

These 32 series form a matrix with gaps that are represented by blank rectangles and are sorted from highest resolution (yellow) to lowest resolution (green) (1).

CLUSTAL W version 2.0.12 [ 64] was used to align each of these 13 genes, using the Gonnet series protein matrix, with a gap opening of 10 and gap extension penalty of 0.2.

Alignment parameters were set to BLOSUM protein weight matrix with a gap opening penalty set to 10.0 and gap extension penalty set at 0.05.

For all these benchmarks, the BLOSUM62 scoring matrix with the gap penalty of 10 and 1 for the Gap Opening and Gap Extension, respectively, is selected.

Protein weight matrix Gonnet, with Gap Opening 10 and Gap Extension 0.2 was used for multiple alignments that were manually refined in GeneDoc v.2.7.0 [34].