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In situations of data super-abundance, a quick π ⁁ d scan could be used to guide subsequent, more detailed alignment-based investigations.
More detailed sequence alignments resulted in design of peptides with better cluster binding features that mimic FA and FB of photosystem I. Other peptide models have also been made to analyze reduction potential properties of different Fe S clusters, including [4Fe 4S] clusters, [2Fe 2S] clusters, and rubredoxins.
Analysis of such data with pid could be an early step followed by more detailed investigations using alignment-based methods.
A more detailed study of local alignment quality then allowed us to highlight a number of differences in the MSA methods tested.
For a more detailed description of the alignment and phylogenetic results, see Additional File 1.
We agree that the description of the method was rather cryptic and we have written a clearer and more detailed description of the alignment procedure.
However, more detailed examination of those alignments and trees disclosed problems in the alignments for all of the candidate novel sequences.
We have rewritten a more detailed description of the two color alignment procedure (See Materials and methods: "Two color alignment procedure").
More detailed phylogenetic analyses with a reduced alignment set (22 cysteine proteinases) were performed by NJ and maximum parsimony (MP) methods.
Phylogenetic data is available in the TreeBASE as accession number S18584 (http://purl.org/phylo/treebase/phylows/study/TB2 S18584), and more detailed information for the marker sequence alignment and phylogenetic analysis could be also available from the Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.org/10.5061/dryad
In this paper, we give an alignment method that makes more detailed use of the path of the projected center of mass along many cross-sections of the object, perpendicular to the axis of rotation.
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