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Complete BLAST alignments are displayed in Figure 3D.
As illustrated in Additional file 5 where these 21 protein alignments are displayed, in most cases, this protein polymorphism corresponded to a variable number of repeated elements or to amino acid variations in these repeat elements.
All motifs and alignments are displayed in the Figures using WebLogo [ 75] For all genes in the Genome Browser RefSeq transcript list, the software R, with the "annotate" and "XML" packages was used to search each abstract of the references listed in the PubMed report for this gene.
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Alignments were displayed in GeneDoc (www.psc.edu/biomed/genedoc), edited and percentages of sequence identity and similarity were calculated.
Alignments were displayed in GeneDoc (http://www.psc.edu/biomed/genedoc), manually edited and percentages of sequence identity and similarity calculated.
Information for these sequences is listed in Tables 1, 2 and 4 and a multiple protein sequence alignment is displayed in Figure S1.
All alignments are displayed using Bioedit Sequence Alignment Editor graphic display [ 87].
The ratios of syntenic to non-syntenic region alignments for each category of annotation are displayed in Figures 6 and 7.
The structural and sequence alignments with the top three Dali server hits are displayed in Figure 1 figure supplement 2 and are described in the Results section.
The alignment as well as list of missing residues are displayed in the browser window and are also made available for downloading.
The resulting alignments were displayed with Jalview [43].
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