Sentence examples for matrices for sequence from inspiring English sources

The 'galign' alignment tool does not use Smith-Waterman matrices for sequence comparisons.

General time reversible models (GTRs) were applied with the corresponding 4 × 4 and 12 × 12 substitution matrices for sequences and sequences-structures, respectively.

It allows users to submit the sequence in FASTA format and choose the user-defined parameters including E -value cutoff, and the substitution matrix for sequence alignment.

The kernel CCA can be given by solving a generalized eigenvalue problem: where I denotes the identity matrix, K exp is the kernel matrix for expression profiles, and K seq is the kernel matrix for sequence motifs.

In our work, we applied BLOSUM62 matrix, a popular substitution matrix used for sequence alignment of proteins, to this transformation.

For instance, a BLOSUM (blocks substitution matrix) is a substitution matrix used for sequence alignment of proteins and it records a score for each of the 210 possible substitution pairs of the 20 standard amino acids.

20 ng DNA of PCR products were used as a matrix for sequencing reaction.

A custom script extracted the longest assembled sequence corresponding to each exon and constructed matrices for multiple sequence alignment, while adding Ns to the matrix if an exon was missing for a particular species.

In the computational biology domain, comparative genomic analyses of transmembrane proteins must be managed with caution because transmembrane regions often possess highly repetitive sequences that are commonly ignored (masked) by conventional sequence comparison tools and that therefore require specialized substitution matrices for proper sequence alignments.

We had proposed a PB substitution matrix (PB SM) similar to a matrix used for sequence alignment.

We believe that with readily accessible modern computing power, it is now feasible to estimate and use organism specific empirical matrices for protein sequence analysis using powerful statistical techniques.