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  1. Jalview
  2. JAL-4219

Parse RNA secondary structure annotation from 'extended' fasta-style files

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      Description

      Often, fasta files output by secondary structure annotation tools include annotation directly following each block of sequence:
      e.g. https://redfold.ee.ncyu.edu.tw/redfold/
      >tdbD00002586
      GCUCGCGUGGCGUAAUGGCAACGCGUCUGACUUCUAAUCAGAAGAUUAUGGGUUCGACCCCCAUCGUGAGUG
      (((((((..((((.......)))).(((((.......))))).....(((((.......)))))))))))).

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          Epic - Created by Jira Software - do not edit or delete. Issue type for a big user story that needs to be broken down. JAL-4147 sub-labels for annotation rows

          • Major - Major loss of function.
          • In Progress
          related with

          New Feature - A new feature of the product, which has yet to be developed. JAL-1052 parse secondary structure from locarna clustalw style RNA alignments

          • Major - Major loss of function.
          • Resolved

          Bug - A problem which impairs or prevents the functions of the product. JAL-3365 Secondary structure annotation beyond DSSP-3 state interpreted as RNA extended base pair contacts in Stockholm files

          • Blocker - Blocks development and/or testing work, production could not run.
          • Open
          mentioned on

          GitLab Merge request - Draft: JAL-4219 - add support for parsing extended fasta files with rna_ss notation

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              Assignee:
              Unassigned Unassigned
              Reporter:
              jprocter James Procter
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                Created:
                Updated: