It is designed to scale to alignment sets of 10 or more base pairs, which is typical for the deep resequencing of one human individual.
For example, the existing alignment sets of 28 mammalian species (Miller et al., 2007) and 46 vertebrate species (Fujita et al., 2011) occupy several hundred gigabytes of disk space and contain millions of alignment blocks.
In order to evaluate the power of our identification method, simulations were performed using sequence alignment sets of random sequences, each consisting of 100,000 pairs of around 5,000 bp sequences and including an inversion in each pair.
Using a previously published method [ 20, 30, 31] which employs single-linkage clustering on top of BLASTp alignments, sets of pan- and core-genomes were estimated, based on all 73 Salmonella genomes.
We applied Friedman rank sum tests to each alignment set with a fixed number of sequences.
Starting from this alignment, a set of 10 full-atoms models was generated for each human monomer.
For the alignment sets, we generated control sets of shuffled alignments.
MAKER2 provides both a conservative biological sequence (transcript and homolog) alignment-based set of gene models that best agree with transcript and protein homolog alignments, and a set of ab initio gene predictions that do not overlap the biological sequence alignment-based set.
For each of the alignments, a set of all Micromonas (Prasinophyceae) sequences available in the ITS2 database was used as the outgroup.
However from a structural point of view even with inconsistent alignments the set of residue equivalences is usually sufficient to produce a good score.
