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  1. Jalview
  2. JAL-886

fetching EMBL reference for an RNA sequence results fails with a sequence mismatch

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      Description

      Looking up database entries for RNA sequences assumes that the database holds an exact match, rather than the genomic version of the sequence.

      E.g.

      >ABJT01000033.1/33739-33825
      AACACAUCAGAUUUCCUGGUGUAACGAAUUUUUUAAGUGCUUCUUGCUUAAGCAAG-UUUC-AUCC-CGACC
      CCCUCA-------GGG-UCGGGAUUU

      Fetching [EMBL database references] for the above (by importing the fasta file above to Jalview, then using fetch db refs->EMBL) results in a 'Sequence not 100% match' error, and no identifier added to the sequence. The database ref fetcher needs to be taught how to translate between DNA and RNA nucleotide sequences.

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          blocks

          Improvement - An improvement or enhancement to an existing feature or task. JAL-1597 more efficient resolution of IDs when querying contig databases

          • Major - Major loss of function.
          • Open
          depends on

          New Feature - A new feature of the product, which has yet to be developed. JAL-1000 translate between DNA and RNA versions of nucleotide sequence

          • Critical - Crashes, loss of data, severe memory leak.
          • Open
          related with

          Bug - A problem which impairs or prevents the functions of the product. JAL-851 sequence database accessions not imported when fetching alignments from Rfam

          • Critical - Crashes, loss of data, severe memory leak.
          • Resolved

          New Feature - A new feature of the product, which has yet to be developed. JAL-1708 resolve cross-references between RNA, DNA, RFAM and 3D coordinates via RNACentral

          • Major - Major loss of function.
          • Open

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              Assignee:
              gmungoc Mungo Carstairs
              Reporter:
              jprocter James Procter
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                Created:
                Updated: