It is aware that these alignments are wrong by assigning low mapping quality, but the true alignments are missed anyway.
We want to use secondary structure information wherever we have both residues in a base pair, but revert to primary sequence alignment when we are missing sequence data.
However, the pattern of gappiness seen in a superalignment (concatenated alignment), where some genes are missing from some taxa, differs from the pattern of gappiness due to partial gene sequences.
Taking into account that for some taxa a few short fragments are missing, the alignments of the non-coding intron regions are 387 bp for GAPDH (the individual sequences ranged between 247-269 bp), and 685 bp for ODC (ranging between 577-619 bp for all taxa, except Corvus that, due to a large deletion, is only 429 bp).
As this alignment shows, the TR3-like enzymes are missing residues Trp407′, Asn418′, and Asn419′ that were proposed to be critical for holding the C-terminal tail of TR1 in one of three positions favoring interaction with the N-terminal dithiol or alternatively with Trx.
We noted that, for reasons unknown, the sixth alignment position is missing in the REP alignment; since there is little conservation at the N-terminus of the repeats, this should have only minimal effect on an analysis using the REP alignment.
273 genes were not mapped because an alignment file was missing.
DNA sequence data are those published in Liti et al [ 14] and only 13-15 loci were available for S. paradoxus because PALAS alignment data were missing for all strains of S. paradoxus for CEN8 and because of low coverage of the American strains for CEN7, CEN8 and CEN12.
Network alignments are noisy and contain both false-positive (defined as aligned pairs that are not functionally related), as well as false-negatives (pairs of functional orthologs that are missed in the alignment).
Further investigation of the functional motifs of TRM4A and TRM4B by sequence alignment demonstrated that TRM4A is missing motif I (Additional file 1: Figure S4A).
