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. 2011 May 21;12:184. doi: 10.1186/1471-2105-12-184

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Copyright © 2011 Anderson et al; licensee BioMed Central Ltd.

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

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MSA comparisons for simulated lipocalin-superfamily protein sequences. Twenty-three protein sequences of the lipocalin superfamily were simulated using iSGv2.1. Simulated sequences were aligned using ClustalW2 v2.1, MAFFT v6.846, and MUSCLE v3.8.31. Panel A shows the comparison of the MSA reconstructed by ClustalW2 against the true alignment provided by iSGv2.1 (the reference alignment) using the MSA Comparator. The column-wise SPS along with the information content for each alignment are displayed between the two alignments,. In Panel B, the Pixel Plot is used to compare the three reconstructed MSAs (MSAs 2-4) against the reference alignment (MSA 1).