Sentence examples for using a substitution matrix from inspiring English sources

Similarity scores are computed by detecting common patterns between two sequences and scoring them using a substitution matrix, with a consistent normalization scheme.

The Smith-Waterman method is a well-established dynamic programming algorithm for finding the optimal local alignment between two sequences using a substitution matrix and a gap-scoring system.

Now imagine that you replace these six sequences with a different set that nevertheless has identical percent identity and similarity as the original set (perhaps as measured by an alignment score using a substitution matrix).

We argue that MIQS can be useful for other database searches, and that this matrix can be influential for the improvement of sophisticated methods, such as PSI-BLAST and profile profile comparison methods, in addition to any method using a substitution matrix in the field of bioinformatics.

Each alignment program has to use a substitution matrix for replacement of characters during the alignment process.

This finding is expected to have a major influence on any field of protein sequence analysis that uses a substitution matrix, such as multiple alignment, profile profile alignment and phylogeny inference.

The statistical significance threshold for including a sequence in the model (E-value) used by PSI-BLAST in the next iteration was either 10-2 or 10-3, BLOSUM45 was used as a substitution matrix.

To make comparison, we also apply Needleman-Wunsch algorithm to align two sequences using BLOSUM62 as a substitution matrix, and calculate the sequence identity as the percentage of aligned part between these two sequences.

This conclusion is supported by amino acid substitution rates inferred separately for the glob1, glob2 and glob3 clades from pairwise within-group sequence comparisons using a PAM substitution matrix and assuming the Drosophila divergence times suggested by Tamura et al. [ 20].

On this set of remote homologues, the more expensive method does not produce better alignments than those using a conventional substitution matrix.

We simulated random mutations by using a compositional substitution matrix based on the nucleotide frequencies of the original (wild type) genome [ 47].