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Comment
. 2015 Jan 13;112(2):E101.
doi: 10.1073/pnas.1419351112. Epub 2015 Jan 6.

Reply to Tan et al.: Differences between real and simulated proteins in multiple sequence alignments

Kieran Boyce  1 , Fabian Sievers  1 , Desmond G Higgins  2
Affiliations
Comment

Reply to Tan et al.: Differences between real and simulated proteins in multiple sequence alignments

Kieran Boyce et al. Proc Natl Acad Sci U S A. .
No abstract available

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.
Fig. 1.
The length of the longest sequence in a protein family is given along the x axis; length of the final alignment is along the y axis. The alignments were produced using the phylogeny-aware program PAGAN. The 41 HomFam datasets (HF), as used in figure 5 of Boyce et al. (2), are rendered as solid squares; the 200 simulated datasets (Sim), as used in Tan et al. (1), are shown as open circles. The average pairwise identity in the alignments is rendered with color (blue/green, high identity; red/yellow, low identity). Lines represent average “inflation” of the alignments because of the alignment process: solid line 40-fold inflation for HomFam, dotted line 12-fold inflation for the simulated data.
See this image and copyright information in PMC

Comment on

References

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    1. Boyce K, Sievers F, Higgins DG. Simple chained guide trees give high-quality protein multiple sequence alignments. Proc Natl Acad Sci USA. 2014;111(29):10556–10561. - PMC - PubMed
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    1. Chang MSS, Benner SA. Empirical analysis of protein insertions and deletions determining parameters for the correct placement of gaps in protein sequence alignments. J Mol Biol. 2004;341(2):617–631. - PubMed
    1. Sievers F, Hughes GM, Higgins DG. Systematic exploration of guide-tree topology effects for small protein alignments. BMC Bioinformatics. 2014;15(1):338. - PMC - PubMed

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