Movements within the scoring matrix correspond to the following alignment actions: An optimal alignment it A of contact maps is a mapping A i, j)=(a(i), b j)) of the pair of (i, j) indices from a complex C onto the (k, m) pair in a complex D where (k, m)=(a(i), b j)).
Sequences were aligned using ClustalX [79], [80] with the following Multiple Alignment Parameters: Gap Opening Penalty: 10.00, Gap Extension Penalty: 0.20.
Nucleotide sequences were analysed and interpreted using Sequencher (Version 5.1, Gene Codes Corporation) and aligned relative to the rCRS [5] following phylogenetic alignment rules defined in [6].
If new residues can be added following an alignment then the expanded set Sn is used to re-align the structures.
The Greengenes 16S rRNA gene database was used for 16S rRNA phylogenetic analysis with the following alignment parameters: >97% identity, minimal alignment 40 bp.
Notably Bfast, Nextgene, Stampy, Mosaik and Bowtie 2 all showed obvious increases in the number of downstream false positives detected following paired-end alignment vs single-end alignment.
Orthologous coding sequences without signal peptides were aligned following the protein alignment by ClustalW (www.ebi.ac.uk/clustalw/).ac.uk/clustalw/
In letters to the Indian prime minister, Jawaharlal Nehru, the Chinese prime minister, Zhou Enlai, quoted a map in the 1929 edition of Encyclopædia Britannica showing the disputed territory as Chinese, with the boundary following the alignment of Chinese maps.
