Stem Loc

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stem loc

[stem loc stemloc] is a program for multiple alignment of RNA using Stochastic Context Free Grammars.

Stemloc uses "alignment envelopes" and "fold envelopes" to simultaneously constrain both the alignment and the secondary structures of the sequences being compared, rendering the RNA comparison problem tractable on commodity hardware.

Related programs

Multiple alignment modes

The first step performed by stemloc is always an "all vs all" pairwise alignment. This uses a constrained version of Sankoff's algorithm for pair SCFGs.

The next step depends on the mode:

  • Progressive Mode is an alternative, single-linkage clustering mode for multiple alignment. Unlike sequence annealing mode, progressive mode tries to give a good consensus alignment and structure, but the resultant alignment is consequently not as good. Progressive mode has the following sub-modes...

Tutorials

StemlocTutorial.small-rd0260-rd0500-na200.png

Download

Stem Loc may be built from source by downloading and compiling DART. See Downloading Dart and Building Dart.

References

Stemloc:

Alignment envelopes:

  • Holmes, I. PhD thesis. Dept of Genetics, University of Cambridge; Wellcome Trust Sanger Institute. 1998. TWikiDocGraphics.pdf.gif (pdf) TWikiDocGraphics.zip.gif (ps.gz)

Fold envelopes: