Sentence examples for matrices and gap from inspiring English sources

Qiu, J. & Elber, R. SSALN: an alignment algorithm using structure-dependent substitution matrices and gap penalties learned from structurally aligned protein pairs.

We intentionally used known substitution matrices and gap scores as parameters to illustrate the link to classical global alignments.

PPM attempts to measure the evolutionary cost of transforming one structure into another by means of residue substitutions, insertions and deletions, thus emulating amino acid sequence comparison using amino acid exchange matrices and gap penalties [23].

Multiple sequence alignment of the Ciona sequences with known orthologs picked up from the gpDB database was performed using CLUSTALX 1.8 program [21] using the default parameters for substitution matrices and gap penalties.

Each MSA program parameterization, such as the choice of substitution matrices and gap opening/extending penalties for example, when available, also strongly affect the final alignment [ 24].

Therefore, substitution matrices and gap penalties tuned to a particular alignment purpose, e.g. contig or short/long-read alignment, can be used unchanged.

The performance order of parameters – like nucleotide substitution matrices and gap-costs – as well as of programs is rated by rank tests.

Correspondingly, we also identified the most sensitive matrix and gap penalties for the SCOP40-v subset.

Similarity Matrix and Gap penalties (Fig. 1 top middle): The user can visualize and modify the values in the similarity matrix and the gap opening/extension penalties.

Redundant sequences were removed after multiple alignments using Multalin [ 33] and ClustalW [ 34] with various parameters (matrix and gap penalties).

It will be accepted that the substitution weight matrix and gap penalties are fixed (see subsection 2.3).