Sentence examples for multiple alignment given from inspiring English sources

Algorithms for finding a multiple alignment given a common structure, i.e. P(A|S,Q), have also been developed.

The likelihood is calculated as the probability of obtaining the data (multiple sequence alignment) given the model of evolution (substitution model and phylogeny).

The original multiple sequence alignment gives rise to a distance matrix D. Each replicate dataset created by sampling columns with replacement from the alignment also gives its corresponding matrix B of perturbed pairwise distances.

Given two column vectors q and q′ of nucleotides and gaps from the query multiple alignment and given two nucleotides t and t′ from the target, f q (t) denotes the frequency of t in q; f q, q ′ (t, t ′ ), the frequency of pairs t and t′ in the corresponding rows of q and q′.

A pseudo-code description of the complete algorithm for multiple alignment is given in Figure 1.

For the five studied GH families, here subdivided into seven different sub-families, amino acid sequences were collected and aligned (multiple alignments are given in Supplementary Figures S1 S7).

Summary: Infernal builds probabilistic profiles of the sequence and secondary structure of an RNA family called covariance models (CMs) from structurally annotated multiple sequence alignments given as input.

This comparative study (Table S3) shows that all the multiple alignment programs gave similar results in terms of sensitivity and specificity, whether launched after GROUPER or after PILER.

The compatibility criterion detected breakpoints by identifying neighbouring sites in the multiple alignment that gave incompatible phylogenetic signals.

The multiple alignments are given in Dataset S5.

Also, the names of the supporting data files containing the corresponding trimmed multiple alignments are given.