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  1. Jalview
  2. JAL-2138

Remove EMBLCDS as a database source

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    Details

    • Type: Task
    • Status: Open
    • Priority: Minor
    • Resolution: Unresolved
    • Affects Version/s: 2.10.0
    • Fix Version/s: None
    • Component/s: data retrieval services, jvdesktop
    • Labels:
      None

      Description

      Since JAL-1855, the URL for EMBL or EMBLCDS retrieval is the same:
      http://www.ebi.ac.uk/ena/data/view/x53828&display=xml // EMBL
      http://www.ebi.ac.uk/ena/data/view/caa37824&display=xml // EMBL CDS

      The former returns the full mRNA including UTR, the latter the coding sequence only.
      In both cases the CDS location is given as X53828.1 [60..1058].
      See comment for today's date on JAL-2114 for discussion of parsing this correctly.
      Regardless of this, there seems to be no reason to retain EMBLCDS as a distinct database source.

        Attachments

          Issue Links

          related with

          Task - A task that needs to be done. JAL-1855 Update to latest version of ENA fetch service

          • Major - Major loss of function.
          • Closed

          Bug - A problem which impairs or prevents the functions of the product. JAL-2110 Duplicate uniprot entries from Ensembl->Show cross-refs->Uniprot

          • Major - Major loss of function.
          • Closed

          Task - A task that needs to be done. JAL-3692 Update ENA endpoint for EMBL/CDS sequence retrieval

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

            Activity

              People

              Assignee:
              jprocter James Procter
              Reporter:
              gmungoc Mungo Carstairs
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                Dates

                Created:
                Updated: