Local Mode

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A local Multiple RNAAlignment mode for Stem Loc. Does not attempt to align the entire sequence (in contrast to Global Mode).

Local Mode can be used with the following options:

  • Progressive Mode - greedy progressive alignment
    • Liberal Mode - length of initial pairwise seed alignment is allowed to increase during progressive extension
    • Conservative Mode - length of initial pairwise seed alignment is fixed
  • Profile Mode - profiling alignment using Covariance Models

See also Global Mode.

-- Ian Holmes - 05 Apr 2005