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In addition, we have modelled the server output to enable comprehensive visualisation of the generated alignment and easy figure generation for publications.
The generated alignment files were examined for general statistics, e.g., number of mapped reads, coverage, insert-size distribution using the sam-stats program from the ea-utils package, and custom scripts (Aronesty 2011).
MUSTANG generated alignment and superposition (NCORE = 143; RMSD = 2.7 Å) were sieved by varying RMSD thresholds from 0.2 Å to 2.7 Å. Figure 3 shows the Lesk-Hubbard plot for the serine proteases data set.
The generated alignment was adjusted manually.
PS carried out additional sequence alignments and generated alignment figures.
Analysis of the generated alignment revealed a LTR of a retrotransposon.
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In certain cases, the CLUSTAL generated alignments were manually corrected.
39 The generated alignments were imported to MEGA 5.0 for visualizing the quality of the alignment.
We generated alignments with this program using the same protein isoform combinations as before.
MF identified and characterised LNX orthologs and generated alignments and phylogenetic trees for individual PDZ domains.
BLAST generated alignments are converted in to PIR format using custom-Perl script.
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