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  1. Jalview
  2. JAL-3808

support import of gff2 alignments from exonerate coding2genome and cds2genome

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    Details

    • Type: Improvement
    • Status: Ready for testing
    • Priority: Major
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: 2.11.2
    • Component/s: file format issue
    • Labels:
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      Description

      Exonerate's cds2genome and coding2genome modes align transcripts and CDS sequences to their locus. The GFF export provides the alignment and (assuming the correct --showtargetgff/--showquerygff option was provided) annotation on the locus identifying exons and splice sites (in the case of 'coding2genome').

      Import of GFF2 files with sequences appended (after ##FASTA) doesn't seem to work reliably for these modes and the GFF2/3 parser for 2.11.1 includes comments suggesting only protein2genome is currently supported.

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            Assignee:
            jprocter Jim Procter
            Reporter:
            jprocter Jim Procter
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              Dates

              Created:
              Updated: