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  1. Jalview
  2. JAL-2353

ignore sequence version numbers in IDs when resolving database references

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    • Sprint:
      2.11.3.0 release

      Description

      Many sequence databases append .X to the accession to indicate the version of the accession from which the sequence data was extracted. Their APIs, however, often do not actually accept ACCESSION.V as a valid accession ID.

      Database clients for ENA, Ensembl,EnsemblGenomes, Uniprot and Uniparc (to name a few) should recognise and strip version numbers before attempting to resolve the ID against their database service.

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          blocks

          Improvement - An improvement or enhancement to an existing feature or task. JAL-3580 allow for sequence mismatches between cross-referenced sequence records according to variant and splice-variant annotation

          • Blocker - Blocks development and/or testing work, production could not run.
          • Open
          is duplicated by

          Bug - A problem which impairs or prevents the functions of the product. JAL-4081 'Get Cross-References' produces HTTP 400 errors with Ensembl queries

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-4469 Handling versioned UniprotKB accessions

          • Minor - Minor loss of function, or other problem where easy workaround is present.
          • Ready for testing
          related with

          Bug - A problem which impairs or prevents the functions of the product. JAL-3076 Gene retrieval from Ensembl 7.0 fails to add features

          • Major - Major loss of function.
          • Closed

          Improvement - An improvement or enhancement to an existing feature or task. JAL-3077 Capture correct accession version when retrieving from Ensembl

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

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              Assignee:
              jprocter James Procter
              Reporter:
              jprocter James Procter
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                Dates

                Created:
                Updated:
                Resolved: