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  1. UGENE
  2. UGENE-137

Add ambiguous bases compatibility to search pattern and Smith-Waterman

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    Details

    • Type: Improvement
    • Status: Closed
    • Priority: Major
    • Resolution: Fixed
    • Affects Version/s: None
    • Fix Version/s: 1.9.4
    • Component/s: Basic-Nucl
    • Labels:
    • Affect Type:
      Userdefined

      Description

      Being able to search for patterns with ambiguous bases would be a nice feature (not present for example in Vector NTI 11). That also will solve an issue with the new feature for annotating several patterns (or primers) from a file with Smith-Waterman in workflow designer, as it returns an error (wrong alphabet) if one of the sequences in the list contains a degenerated base (I have several degenerated primers). The way to solve it now is changing those bases for N, but is not accurate and can give false positives. I've been thinking in fast way to implement that without modifying the searching routines. In my opinion, it should search consecutively the different possible sequences. For example, if the pattern to search is AYTTG, then preform the search for ACTTG and then for ATTTG.

      Ambiguous bases:
      M: A or C
      R: A or G
      W: A or T
      S: C or G
      Y: C or T
      K: G or T
      V: A or C or G
      H: A or C or T
      D: A or G or T
      B: C or G or T
      N: G or A or T or C

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            Assignee:
            kokonech Konstantin Okonechnikov
            Reporter:
            agu Agustín Ure
            Watchers:
            3 Start watching this issue

              Dates

              Created:
              Updated:
              Resolved: