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The number of generations and "burn-in" were defined by analysis of multiple sequences, with topological stability assessment by the AWTY package (Nylander et al. [2008]) and analyzed by the parametric stability software, Tracer 1.5.
This progressive alignment efficiently aligns multiple sequences with reasonable accuracy.
Motif-based alignment tool consists of two main parts to align multiple sequences with different affinity scores of STAT TFBSs.
Easyfig accepts multiple sequences with or without annotation in standard formats (i.e. GenBank and EMBL).
Results were verified by comparing with the conservation score calculated by aligning multiple sequences with ClustalW2 [ 34].
The pipeline could further be improved by including methods such as CMfinder [ 60] which can search for RNA structures in multiple sequences with low sequence similarity.
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The rooted tree is based on a multiple sequence with alignment algorithm MAFFT and generated with the program Mega6.
The homologous comparison is based on a multiple sequence with alignment algorithm MAFFT and generated with the programDNAMAN8; b Phylogenic tree of TCD10 and homologs.
Thus, CHST11 activity may lead to larger CS polymers with multiple sequences embedded with distinct sulfation patterns resulted from activity of multiple sulfotransferases, leading to the production of conformational epitopes or highly concentrated sequences with specific reactivities.
Sequences were assembled with BioEdit, and multiple sequences were aligned with Clustal W (http://www.ebi.ac.uk/).ac.uk/
Multiple sequence alignment with known laccases indicated high sequence identity with basidiomycete laccases as compared to the ascomycete laccases.
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