Sentence examples for alignment and modeling from inspiring English sources

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 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.

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.

The sequence alignment and model have several convincing features.

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

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].

A recursive approach comprising of sequence alignment and model building based on three templates was used to build these models, with the refinement of non-conserved regions carried out using threading techniques.

Inspection of the resulting alignment and model showed that while the NBD, HD1 and WH domains (217 632) were clearly homologous between NOD2 and NLRC4, the rest of the exon, which forms HD2 and part of the LRR domain in NLRC4, showed a more ambiguous alignment and so was not considered further.