FAQ

• What is the difference between . and - in alignments ?

In cmalign alignments, - means a nucleotide is missing compared to the covariance model. It represents a deletion. The dot '.' indicates that another chain has an insertion compared to the covariance model. The current chains does not lack anything, it's another which has more.

In the final filtered alignment that we provide for download, the same rule applies, but on top of that, some '.' are replaced by '-' when a gap in the 3D structure (a missing, unresolved nucleotide) is mapped to an insertion gap.

• Why are there some gap-only columns in the alignment ?

These columns are not completely gap-only, they contain at least one dash-gap '-'. This means an actual, physical nucleotide which should exist in the 3D structure should be located there. The previous and following nucleotides are not contiguous in space in 3D.

• Why is the numbering of residues in my 3D chain weird ?

Probably because the numbering in the original chain already was a mess, and the RNANet re-numbering process failed to understand it correctly. If you ran RNANet yourself, check the logs/ folder and find your chain's log. It will explain you how it was re-numbered.

• What is your standardized way to re-number residues ?

We first remove the nucleotides whose number is outside the family mapping (if any). Then, we renumber the following way:

0) For truncated chains, we shift the numbering of every nucleotide so that the first nucleotide is 1.
1) We identify duplicate residue numbers and increase by 1 the numbering of all nucleotides starting at the duplicate, recursively, and until we find a gap in the numbering suite. If no gap is found, residue numbers are shifted until the end of the chain.
2) We proceed the similar way for nucleotides with letter numbering (e.g. 17, 17A and 17B will be renumbered to 17, 18 and 19, and the following nucleotides in the chain are also shifted).
3) Nucleotides with partial numbering and a letter are hopefully detected and processed with their correct numbering (e.g. in ...1629, 1630, 163B, 1631, ... the residue 163B has nothing to do with number 163 or 164, the series will be renumbered 1629, 1630, 1631, 1632 and the following will be shifted).
4) Nucleotides numbered -1 at the begining of a chain are shifted (with the following ones) to 1.
5) Ligands at the end of the chain are removed. Is detected as ligand any residue which is not A/C/G/U and has no defined puckering or no defined torsion angles. Residues are also considered to be ligands if they are at the end of the chain with a residue number which is more than 50 than the previous residue (ligands are sometimes numbered 1000 or 9999). Finally, residues "GNG", "E2C", "OHX", "IRI", "MPD", "8UZ" at then end of a chain are removed.
6) Ligands at the begining of a chain are removed. DSSR annotates them with index_chain 1, 2, 3..., so we can detect that there is a redundancy with the real nucleotides 1, 2, 3. We keep only the first, which hopefully is the real nucleotide. We also remove the ones that have a negative number (since we renumbered the truncated chain to 1, some became negative).
7) Nucleotides with creative, disruptive numbering are attempted to be detected and renumbered, even if the numbers fell out of the family mapping interval. For example, the suite ... 1003, 2003, 3003, 1004... will be renumbered ...1003, 1004, 1005, 1006 ... and the following accordingly.
8) Nucleotides missing from portions not resolved in 3D are created as gaps, with correct numbering, to fill the portion between the previous and the following resolved ones.

• What are the versions of the dependencies you use ?

cmalign is v1.1.4, sina is v1.6.0, x3dna-dssr is v1.9.9, Biopython is v1.78.