Sentence examples for alignment and modelling from inspiring English sources

Therefore we employed an alignment procedure that uses a linear Hidden Markov Model (HMM) as implemented in the software SAM (Sequence Alignment and Modelling system) [ 84] for separate alignments of the three data sets.

V-H+PPases: Vacuolar proton-translocating pyrophosphatases; Pfam: Protein family; LUCA: Last universal common ancestor; LGT: Lateral gene transfer; PDB Protein Data Bank HMMs Hidden Markov Models SAM Sequenceuence alignment and modeling system The authors declare that they have no competing interests.

The multiple sequence alignment and model of the CMTr2 catalytic domain structure were also used to plan site-directed mutagenesis experiments.

The simplest is POA (Partial-Order Alignment); a similar but more generalized method is implemented in the packages SAM (Sequence Alignment and Modeling System).

We downloaded the set of models (version 1.69) and used them in connection with the Sequence Alignment and Modeling system (SAM, version 3.5), recommended by the creators of the SUPERFAMILY database.

The sequence alignment and model have several convincing features.

Sequence alignment and model specification proceeded as described above, unless otherwise stated.

A profile HMM was built using these sequences with the Sequence Alignment and Modeling System (SAM) [ 99, 100].

The Sequence Alignment and Modeling System program (SAM Version 3.5– T2K) [ 29] was used to predict the remote intermediates.

The program package, Sequence Alignment and Modeling System (SAM, version 3.5) [ 24, 25] is used for implementing profile HMMs.

Two models were compared by an LRT test: model M7, assuming no positively selected sites in the alignment, and model M8, which allows for their existence [ 40, 41].