Sentence examples for training alignments from inspiring English sources

After the initial DTs are constructed from the training alignments, the HMM transition parameters and DT leaf values are re-estimated using several iterations of the Baum-Welch algorithm [1].

This yields a dataset of negatives, or alignments with statistical properties similar to those of the original training alignments but with no true ncRNAs present.

We fitted newly estimated HIV models and three previously published models-JTT [28], WAG [14] and rtREV [15], estimating stationary frequencies from the data to each of the training alignments.

We developed an efficient computational tool to facilitate the estimation of substitution matrices from training alignments and subsequent generation of scoring matrices at the desired level of evolutionary distance.

HyPhy scripts needed to fit a REV model to a collection of training alignments and generate similarity scoring matrices can be downloaded from http://www.hyphy.org/pubs/HIV-model/. HIV-1 models presented here are available as a part of the standard distribution of HyPhy (HIVWithin and HIVBetween models).

The training alignments and test fragments are provided in the Supplementary Material.

It is composed of a set of 106 families, each represented by a training alignment of ≥5 aligned sequences and a test set of ≥1 sequences.

We aligned each test sequence fragment to the training alignment using four different local alignment methods.

Hamada, M., Ono, Y., Asai, K. & Frith, M. C. Training alignment parameters for arbitrary sequencers with LAST-TRAIN.

The number of sequences a training alignment contains is limited to 6 as the SVM regression procedure to estimate the z-scores is trained with alignments of maximal 6 sequences [ 15].

For the subtree-based local alignment method, we used Infernal version 1.0 to build a CM of the training alignment subset with cmbuild with the –enone option to shut off entropy weighting.