Opened 6 years ago

#250 new task

import/export for secondary structures

Reported by: westram Owned by: devel
Priority: normal Milestone:
Component: ARB_NTREE Version:
Keywords: Cc:

Description

for some ss-format-examples

Problems:

  • ARB helix numbering will be lost when doing export+import
  • has to be alignment-independent to import correctly after inserting/deleting gaps
    • some formats use one reference sequence (for prediction software this is the sequence on which the prediction has been calculated) - fine for importing that structure
    • when exporting, ARB would need a sequence which is covering all helix-columns (it's quite unlikely that such sequence exists)

Possible solutions:

  • cook own reimportable format
    • save helix-names
    • save a set of sequences, such that for each helix column at least one of them has data
      • may still be impossible (if no seq has data at one helix position)
      • can only be imported, if all sequences of the set exists in the target DB

ideas anybody?

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