If there is more than one local alignment in a gene pair, we used the most conserved alignment.
For the two most conserved alignment classes, we analyzed the persistence of the sequence similarity in more distantly related species.
In addition, for the most conserved Cons alignments (>86% identity over alignment length) the fraction of human-specific positively selected genes was very similar for Cons and PALO (∼0.7%) but still more than double for Longest (∼1.6%).
For the most conserved class of vertebrate alignments, 58% of non coding regions are alignable between human and fish, versus 95% of coding alignments (66.48% identity in alignable non coding sequences, 69.23% in alignable CDS).
Ribosome is the largest, central cluster identified in the alignment graph of core genes, and together with proteasome and spliceosome, constitutes the three most conserved complexes in the alignment graph.
In particular, our findings show that a nucleotide preferred at some position of a multiple alignment of binding sites for some transcription factor in the same genome is not necessarily the most conserved nucleotide in an alignment of orthologous sites from different species.
The most conserved parts of the alignment are shown on Figure 2. The fragment of Leifsonia xyli CTCB07 genome [GenBank: NC_006087] revealed by Genomic BLAST has 2 stop codons in the region homologous to genes of GH97 family proteins.
For each shortening step, two data partitions were obtained: 1) the shortened alignment containing the most conserved sites (partition "A") and 2) an alignment containing the more varied sites (partition "B").
However, the sequences used in this study correspond to coding sequences from which we extrapolated their most conserved parts (cores) to perform alignments.
Using the pairwise data, start and end positions of the modules were estimated from the many alignment regions and were set to cover as much of the sequence as possible, not only the most conserved regions of all the alignments.
