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The multiple alignment diagram of the new Alu subfamilies discovered in this study was constructed using the "view alignment report" option in MegAlign with the ClustalW algorithm followed by manual formatting of "alignment report contents" under Options (DNASTAR, Inc. Version 5.0 for Windows).
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This gene is indicated as Bf.SelP_a in the gene structure schematic diagram (Additional file 1: Figure S1) and multiple alignment (Additional file 1: Figure S2).
Multiple protein structural alignments were performed using MUSTANG (http://lcb.infotech.monash.edu.au/mustang), with the corresponding sequence alignment diagram prepared by using Chimera (https://www.cgl.ucsf.edu/chimera).ucsf.edu/chimera
An algorithm for progressive multiple alignment of sequences with insertions.
(c) Multiple alignment of the NREP ORF across vertebrates.
Multiple alignment analysis was performed using Multalin (http://multalin.toulouse.inra.fr/).inra.fr/
It then constructs a multiple alignment that is maximally consistent with the improved pairwise alignments.
Schematic band alignment diagram for the interface of these hetero-structures has been constructed.
Sequence alignments, hidden Markov models, multiple alignment algorithms and heuristics such as Gibbs sampling, and the probabilistic interpretation of alignments will be covered.
multiple alignment using fast Fourier transform.
Subsequently, multiple alignment analysis was performed with DNAMAN 6.0 software.
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