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  1. Jalview
  2. JAL-2079

RFAM and PFAM sequence fetching sites are discontinued (sanger.ac.uk)

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    Details

    • Type: Bug
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: 2.9.0b2
    • Fix Version/s: 2.10.0
    • Component/s: data retrieval services
    • Labels:
      None

      Description

      http://pfam.sanger.ac.uk and http://rfam.sanger.ac.uk are discontinued services. Jalview reports error "Didn't retrieve following query..." when attempting to fetch example from PFAM or RFAM sources.

      For sequence fetching, we must now use http://pfam.xfam.org and http://rfam.xfam.org.
      Source files that hardwire PFAM/RFAM web sites need to be updated:
        PfamFull.Java
        RfamFull.Java
        PfamSeed.Java
        RfamSeed.Java

        Attachments

          Issue Links

          related with

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2180 External database not available failure message

          • Major - Major loss of function.
          • Open

          Improvement - An improvement or enhancement to an existing feature or task. JAL-2084 Rfam full alignments are no longer available

          • Major - Major loss of function.
          • Closed

          Epic - Created by Jira Software - do not edit or delete. Issue type for a big user story that needs to be broken down. JAL-2182 recognise and update out of date URLs associated with databases and annotation

          • Major - Major loss of function.
          • Open

            Activity

              People

              Assignee:
              jprocter James Procter
              Reporter:
              stuarto Stuart Ozer
              Votes:
              1 Vote for this issue
              Watchers:
              3 Start watching this issue

                Dates

                Created:
                Updated:
                Resolved: