Sentence examples for matrix and gap from inspiring English sources

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

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).

The alignment was analyzed for recombination by Recco [ 41] with the Hamming mutation cost matrix and gap extension costs of 0.2.

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.

In searches for divergent homologues, the statistical significance threshold for reporting matches was raised, word size decreased to 2, and matrix and gap costs varied.

(In difference to the algorithm given in [ 1], the algorithm described in [ 5] besides the usual weight substitution matrix and gap-open and gap-extension penalties, requires an additional parameter - constant penalty for each difference block).

Prior to the tests with sequences of variable homology along the sequence, we investigated the dependence of the quality of the alignment on the applied substitution matrix and gap-open and gap-extension penalties.

Sequences were aligned by ClustalW [ 47] using default parameters (a Gonnet protein weight matrix and gap-opening penalties of 10 and gap-extending penalties of 0.1 and 0.2 for pair-wise and multiple alignments, respectively) implemented in the MEGA4 program [ 48].

SEQUOIA uses a conventional dynamic programming algorithm based on the work of Needleman and Wunsch [ 30] to find the globally optimal alignment given a particular residue comparison matrix and gapping model.

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