Dear all,
We are using progressiveMauve to construct multiple alignments for highly
similar (>99.8%) and clonal bacterial genomes. Normally, we would do
subalignments in sets of 10-20 genomes where we include a common reference
genome to support merging the information into a big alignment.
We have recently noted, however, that the number of shared (orthologous)
nucleotide sites in the final alignment actually becomes significantly smaller
when we run the genomes in larger sets. The more genomes included in the
subalignments, the worse the situation gets. We get the best result when we do
subalignments for individual genomes with a reference before merging. Numbers
of homoplastic SNPs in the different alignments appear to remain about the same.
This phenomenon is to me completely contra-intuitive as you would expect that
more genomes in an alignment would enable a more accurate end result.
Has anyone else also experienced this?
Kind regards, Pär
________________________________
Pär Larsson
Research scientist
Department for CBRN Defence and Security
FOI
Swedish Defence Research Agency
SE- 901 82 Umeå, Sweden
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par.lars...@foi.se<mailto:par.lars...@foi.se>
www.foi.se<http://www.foi.se/>
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