Sentence examples for penalty gap from inspiring English sources

The default parameters for gap open penalty, gap extension penalty, and perform fft were used (1.53, 0.12, "localpair").

To investigate whether the set of assembled sequences contain alternative transcripts of the same loci, the contigs and singlets were further clustered using the SeqManII software with the following relaxed parameters: match size = 12; maximum added gap length = 70; minimum percent match = 80; no gap penalty; gap length penalty = 0.70.

The weighing matrix used for ClustalW alignment was BLOSUM with the penalty of gap opening 10 and gap extension 0.2.

Piccolo and Bassoon protein sequences were aligned using MUSCLE (Edgar 2004a, b) with default settings (−2.9 penalty for gap opening, no penalty for gap extension, a 1.2 hydrophobicity multiplier, and UPGMB clustering method).

Multiple alignments of Orc/Cdc6 homologs were generated using Clustal (substitution matrix = BLOSUM; gap-opening penalty =10; gap-extension penalty = 0.1), and the result was adjusted manually to remove columns with many gaps.

The energy thresholds were set at ≤ -20 kcal/mol and other thresholds used a default value (score threshold, 120; gap-opening penalty, -9; gap-extend penalty, -4).

Gap open penalty: 12. Gap extension penalty: 3. Alignment type: Global alignment with free end gaps.

A.m.Mβ': own prediction A.m.Mβ': database prediction Penalties: bestfit: Gap weight: 1, length weight: 1, max.

The RpoB' amino acid sequences were collected, and multiple alignments were generated using Clustal (substitution matrix = BLOSUM; gap-opening penalty = 10; gap-extension penalty = 0.1).

The indicated L2 residues were aligned with the MacVector software ClustalW algorithm using the BLOSUM series matrix with default settings for open gap penalty, extended gap penalty, delay divergent percentage, and protein gap parameters.

The alignment settings were open gap penalty 100%, unit gap penalty 0%, match score 100%, and fast algorithm (= minimum match sequence 2, maximum number of 98).