Louis BECQUEY / RNANet

The first uses of RNAnet by people from outside the development team happened last December. A few feedback allowed to identify issues and useful information to add.

FEATURE CHANGES

• Sequence alignments of the 3D structures mapped to a family are now provided.
• Full alignments with Rfam sequences are not provided, but you can ask us for the files.
• Two new fields in table 'family': ali_length and ali_filtered_length. They are the MSA lengths of the alignment with and without the Rfam sequences.
• Gap replacement by consensus (--fill-gaps) has been removed. Now, the gap percentage and consensus are saved in the align_column table and the datapoints in CSV format, in separate columns. Consensus is one of ACGUN-, the gap being chosen if >75% of the sequences are gaps at this position. Otherwise, A/C/G/U is chosen if >50% of the non-gap positions are A/C/G/U. Otherwise, N is the consensus.

TECHNICAL CHANGES

• SQLite connections are now all in WAL mode by default (previously, only the writers used WAL mode, but this is useless)
• Moved to Python3.9 for internal testing.
• Latest version of BioPython is now supported (1.78)

BUG CORRECTIONS

• When an alignment file is updated in a newer run of RNANet, all the re_mappings are now re-computed for this family. Previously, the remappings were computed only for the newly added sequences, while the alignment actually changed even for chains added in past runs.
• Changed the ownership and permissions of files produced by the Docker container. They were previously owned by root and the user could not get access to them.
• Modified nucleotides were not always correctly transformed to N in the alignments (and nucleotide.nt_align_code fields). Now, the alignments and nt_align_code (and consensus) only contain "ACGUN-" chars. Now, 'N' means 'other' or 'any', while '-' means 'nothing' or 'unknown'.