Uploaded image for project: 'Jalview'
  1. Jalview
  2. JAL-1597

more efficient resolution of IDs when querying contig databases

    XMLWordPrintable

    Details

    • Type: Improvement
    • Status: Open
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: 3.0
    • Component/s: data retrieval services, na
    • Labels:
      None

      Description

      When resolving database references for a DNA or RNA locus Jalview should deal intelligently with ID queries that may result in genomes or chromosomes being retrieved.

      * if the original sequence being resolved has a start position greater then 1, then there is a good chance the sequence limits are actually in an external coordinate system, so try specifying the range in the query.
      * employ an external service to attempt to locate sequence range rather than download and match directly.

        Attachments

          Issue Links

          blocks

          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
          depends on

          Bug - A problem which impairs or prevents the functions of the product. JAL-886 fetching EMBL reference for an RNA sequence results fails with a sequence mismatch

          • Major - Major loss of function.
          • In Progress

            Activity

              People

              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
              Votes:
              0 Vote for this issue
              Watchers:
              1 Start watching this issue

                Dates

                Created:
                Updated: