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  1. Jalview
  2. JAL-2998

Use nhmmer not hmmsearch for nucleotide alignments

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    Details

    • Type: New Feature
    • Status: In Progress
    • Priority: Minor
    • Resolution: Unresolved
    • Affects Version/s: None
    • Fix Version/s: 2.12.0
    • Component/s: jvdesktop
    • Labels:
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      Description

      Although hmmsearch does produce a 'result' when searching nucleotide using a DNA profile, the correct program to run is nhmmer. This is new in HMMER3.1 with the release note
      "HMMER now includes tools that are specifically designed for DNA/DNA
      comparison: nhmmer and nhmmscan. The most notable improvement over using HMMER3’s tools is the ability to search long (e.g. chromosome length) target sequences."

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            Assignee:
            gmungoc Mungo Carstairs
            Reporter:
            gmungoc Mungo Carstairs
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              Dates

              Created:
              Updated: