Percentage of residues that are correctly aligned in pairwise sequence alignments from the BAliBASE reference set 7, sorted by sequence identity of the protein families.

<p>Mean = mean percentage of correctly-aligned residues over averages for eight families. ^aNumber of pair-wise alignments. ^bMean (±standard deviation) of the percentage sequence identity between pairs of alignments in each family.</p

Percentage of residues that are correctly aligned in pairwise sequence alignments assigned to different subgroups within the BAliBASE reference set 7, sorted by sequence identity of the alignments in each protein family.

<p>See legend to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057731#pone-0057731-t004" target="_blank">Table 4</a> for more details.</p

Average shift error in pairwise alignments of the BAliBASE reference set 7.

<p>Families are sorted by the average sequence identity (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057731#pone-0057731-t004" target="_blank">Table 4</a>). Mean = mean over averages for eight families.</p

Percentage of residues that are correctly aligned in pairwise sequence alignments assigned to the same subgroup within the BAliBASE reference set 7, sorted by sequence identity of the alignments in each protein family.

<p>See legend to <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057731#pone-0057731-t004" target="_blank">Table 4</a> for more details.</p

Percentage of residues that are correctly aligned in the predicted transmembrane regions of pairwise sequence alignments from the BAliBASE reference set 7, sorted by protein family name.

<p>Mean = mean over averages for eight families.</p

Average shift error in pairwise alignments assigned to the same subgroup within the BAliBASE reference set 7.

<p>Families are sorted by the average sequence identity (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057731#pone-0057731-t005" target="_blank">Table 5</a>). Mean = mean over averages for eight families.</p

Accuracy of homology models constructed based on HOMEP2 data set alignments from different methods.

a<p>Reference alignments generated by the structure alignment program, SKA. The number of models is shown in parentheses.</p

Percentage of transmembrane segments in the HOMEP2 set that are correctly aligned by each method.

<p>Transmembrane segment definitions are taken from the structures according to the PDB_TM database (see Methods); matching is defined as correct if 50% (<i>f</i>⁵⁰) or 90% (<i>f</i>⁹⁰) of the residues are aligned. Results are sorted according to the level of sequence similarity of the sequence pair. The number of pairwise alignments is shown in parentheses.</p

Comparison of alignment accuracy when using multiple input descriptors in AlignMe.

<p>Combinations included: (a) PSSMs with hydrophobicity descriptors or transmembrane predictions; (b) secondary structure prediction with PSSMs or transmembrane predictions; or (c) PSSMs, PSIPRED and OCTOPUS together. The scores obtained using PSSMs or PSIPRED alone are indicated with gray lines for reference. Gap penalties were assigned differently to sequence segments above or below a threshold (black bars), and the threshold was defined using the inputs marked by *. For example, in the PSIPRED* & OCTOPUS combination, the threshold was assigned using PSIPRED. See legend for <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057731#pone-0057731-g001" target="_blank">Figure 1</a> for further details.</p

Average shift error in pairwise alignments assigned to different subgroups within the BAliBASE reference set 7.

<p>Families are sorted by the average sequence identity (see <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0057731#pone-0057731-t006" target="_blank">Table 6</a>). Mean = mean over averages for eight families.</p