In addition to the baseline three-state model, we have compared our approach to other alignment programs Context [ 15] and Muscle [ 21].
Table 1 Acoustic filtering performed by a simple Viterbi alignment on context-free HMMs (Baseline), with GMM-filtering and ASAP pruning (A-GMM), with ASAP and smart querying coupled with GMM-based filters (A-SR-GMM) and MLP-based filters (A-SR-MLP).
This means that, should both genes be concatenated to form a larger alignment, different context-dependent codon partition models may need to be used for each gene to perform accurate phylogenetic reconstruction for such a concatenated alignment.
As a new contribution, we address a classification algorithm that has a workflow context alignment from the relatedness aspect of workflows.
We show BFAST can achieve substantially greater sensitivity of alignment in the context of errors and true variants, especially insertions and deletions, and minimize false mappings, while maintaining adequate speed compared to other current methods.
We then parsed out the TM profiles for the authority protein and the aligned MoLFunC, and visually superimposed them on the plot so we could see the alignment in the context of the topologies.
Results: We present the first application which allows visualization of conserved regions in a multiple sequence alignment in the context of codons.
This process has many of the hallmarks of interactive alignment in the context of joint action and dialogue (Garrod & Pickering, 2009).
The alignment of gene context / neighborhoods of and around the luxI homologs show conserved topology where novR is proximal to novI and where transcriptional orientation is convergent with the receptor (novR) upstream (of novI), a genomic context feature based on proximity commonly found in complete QS regulatory circuits (luxR and luxI) in the alpha subclass of Proteobacteria.
The intronic architecture of the GHF5 endoglucanase genes was mapped onto a multiple protein sequence alignment in the context of the overall secondary structure of an archetypal GHF5 endoglucanase (See additional file 3), but there appears to be no general correlation.
