Sentence examples for extend gap from inspiring English sources

Sequence identities were calculated using Lalign [19] with the default scoring matrix, an open gap penalty of −14 and an extend gap penalty of −4.

The BLOSUM-62 scoring matrix was used with identical open and extend gap penalties for each alignment.

Sequences were aligned using Clustal W, with a gap penalty of 10, an extend gap penalty of 0.2 and a delay of divergence of 30%.

The blastp algorithm used gapped alignment with the following parameter: expectation value 10-300), open gap (−1), extend gap (−1), threshold for extending hits (11) and word size (3).

Plastid contigs were identified by MegaBLAST searching all contigs against the Solanum lycopersicum L. (AM087200) plastome using an E-value of 1e-10 (Wu et al., 2006), a k-mer length of 24, a scoring match-mismatch of 1-2, and a linear open extend gap cost.

Each N. tabacum exon was separated using the extract annotations feature in Geneious, and these exons were BLASTN searched against S. lycopersicum using an E-value of 1e-10, a k-mer length of 15, a scoring match-mismatch of 2-3, and a 5-2 opextendend gap cost (this BLASTN search is more likely to find matches than the MegaBLAST search used elsewhere).

It is also possible to extend gapped PWMs to incorporate other generalisations of the PWM model such as position dependencies.

Indel detection methods that only employ gapped alignment of short reads to reference are often limited by false positives introduced by systematic, context-dependent sequencing error, and false negatives introduced by failure of the aligner to open or extend gaps.

Two main definitions of treefall gaps exist: canopy gap: a 'hole' in the forest through all levels down to an average height of 2 m above ground and extended gap: canopy gap plus the area that extends to the bases of surrounding canopy trees.

Feeling they could take the joke further, they came up with the first annual Dime Glory Challenge last year, a one-day skate contest centered on the Joe Valdez Challenge, an event where skaters do tricks across an extending gap onto a narrow, 12-inch wide ledge.

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.