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  1. UGENE
  2. UGENE-4067

Align sequences to an existing alignment in the Alignment Editor

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    • Story Points:
      5
    • Sprint:
      DEV-05/03/2015, DEV-10/04/2015, DEV-06/05/2015
    • Affect Type:
      Userdefined

      Description

      Add "Align sequence to this alignment" button to the Alignment Editor toolbar. The behavior of the button should be the following:
      1. If sequences objects are selected in the current project, the sequences are added and automatically aligned to the alignment consensus (no other dialogs are shown):

      1.1. MAFFT algorithm is used when the MAFFT external tool is valid (e.g. it is a valid full UGENE package).
      In the current UGENE version "Accurate aligning" MAFFT option is always used by default (see UGENE-4290 for possible improvement on that).
      If the length of the added sequences is less than 100 and less than 1/3 of the alignment length, "add-fragments" MAFFT option is used (i.e. "Disallow gaps insertion"). Otherwise, "add" MAFFT option is used.

      1.2. A simple alignment algorithm is used otherwise. This happens, for example, if a user uses standard UGENE package.
      The algorithm works as follows. It tries to put the added sequence into each location in the alignment, calculating the similarity between the sequence and the alignment consensus. The locations with the most similarity is chosen as the result. If several locations with the same similarity were found, the sequence is aligned at the first found location.

      2. If sequences were not selected, a dialog for selecting sequences appears. It allows to select files in sequence and multiple alignment formats, for example, FASTA, GenBank, ClustalW, etc.

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              Assignee:
              artyom_s Artyom Savchenko
              Reporter:
              oigl Olga Golosova
              Assigned Tester:
              Aleksey Tiunov [X] (Inactive)
              Watchers:
              3 Start watching this issue

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                Updated:
                Resolved:

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