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An examination of the binding sites used to create the PWMs in the TRANSFAC database suggested that introducing gaps into the middle of binding sites could achieve a better alignment for the whole length of the motif.
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HHALIGN is supposed to produced better alignment scores and better alignments for the best scoring one but also for the other candidates.
This segment-based multiple alignment program is known to produce better alignments for the purpose of phylogenetic footprinting than does the tree-based global multiple alignment program ClustalW [ 43], because it starts by identifying short conserved regions and then incorporates them into a multiple alignment [ 44].
For the HD1/HD2 tree, nucleotide sequences were aligned with MUSCLE [ 72] since it produced a better alignment for such highly divergent sequences.
NIL needs just improvements to defect densities and better alignment for widespread industry adoption.
CDS length in C. reinhardtii genes was positively correlated with both Δ L (ρ = 0.393, P < 10−) and UnalignRes regardless of alignment tool used (ClustalW: ρ = 0.412, P < 10−; MUSCLE: ρ = 0.481, P < 10−), indicating in general there was better alignment for orthologs encoding shorter proteins.
All these concerns notwithstanding, you are never going to have a better alignment of the stars for making a deal than you have now in the Clinton-Arafat-Barak trio.
Current insecure economic context and ongoing needs for more insurance between business partners advocate for a better alignment of the company with newly arising principles of corporate governance of IT.
An appropriate research agenda encompassing the assembly of large and diverse datasets, and an analysis plan involving regression based models will help to provide further insight into the potential for achieving a better alignment of the DAS28 (CRP -defined and the DAS28 (ESR)-defined EULAR response states.
Kalign is faster than ClustalW and produces better alignments for more distantly related sequences.
It is noted that the strips were oriented parallel to the liquid interface for better alignment along the strip direction as shown in Fig. 1b.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com