Sentence examples for alignment matrices from inspiring English sources

We used Megablast [ 30, 31] to align all SDs against each CNV and created 1,447 alignment matrices (see Section 2).

The alignment matrices were analyzed by the maximum parsimony (MP) using PAUP* version 4.0b10 (Swofford 2003) with tree-bisection-reconnection (TBR) branch swapping and the MULTREES (holding multiple trees) option in effect with 1000 replicates of random sequence addition.

MQD is the 4 × 4 matrix used to align D onto Q. MQD is calculated on the fly through the product of the pre-computed query/reference (MQR) and reference/dataset (MRD) alignment matrices.

The program uses multiple sequences of sRNA-specific transcriptional signals in fasta format as input for the construction of alignment matrices.

The LiDAR panorama scans from each scan station were imported into the PolyWorks software package (www.innovmetric.com) and merged to create the alignment matrices for each individual scan station.

We design and implement a HMM and run the HMM on alignment matrices for annotating duplicons.

To model evolutionary constraints (not necessary related to folding) imposed on synonymous variability in different genomic positions (e.g. mutational bias) we maintained the distribution of synonymous codons (and thus nucleotides) for each column in the interserotype multiple alignment matrix (matrix containing aligned sequences of 4 serotypes).

When aligning a pair of sequences, the problem can be represented by an alignment matrix.

A common and popular structural alignment method is the DALI, or distance alignment matrix method, which breaks the input structures into hexapeptide fragments and calculates a distance matrix by evaluating the contact patterns between successive fragments.

First, the sequences were arranged into an alignment matrix, which defined the number of times each nucleotide was found at a specific position within the alignment.

For Patser searches, the a priori nucleotide probabilities used to convert the alignment matrix to a weight matrix were set to 0.25 for all 4 nucleotides.