115 lines
4.4 KiB
Plaintext
Executable File
115 lines
4.4 KiB
Plaintext
Executable File
MFOLD - Prediction of RNA secondary structure by free energy
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minimization.
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- Version 2.0
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- Michael Zuker and John Jaeger
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- lrna : folds linear RNA sequences
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- crna : folds circular RNA sequences
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The original version (1.0) was designed by Michael Zuker and
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programmed by Eric Nelson in the summer of 1987 in the Division of
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Biological Sciences at the National Research Council of Canada. John
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Jaeger added the tetraloop bonus energy feature and created the
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BATGEN program for batch file generation.
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Version 2.0 corrects a number of small bugs from the original
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program. These were added to version 1 and itemized in the
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ERRATA.LIST file that was distributed along with version 1. The major
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improvements of version 2 are :
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1. During the generation of suboptimal foldings, the number of new
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base pairs that are sufficiently different from base pairs that have
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already been found must be greater than the WINDOW parameter. This
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feature was added during the summer of 1989, and was made part of
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version 1 (item 11 in the ERRATA.LIST file distributed with this
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version). The effect is to eliminate structures that contain just a
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few new base pairs.
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2. Temperature dependent folding. This was added in the fall of 1989
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and was never a feature of version 1.
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3. The multiple sequence option will now generate suboptimal foldings
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of all the sequences in an input file. This can be used (for
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example), to compute all foldings within 10% of the minimum energy
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for all the 5S RNAs conained in a single file.
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The programs were adapted to run in a UNIX environment during the
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winter of 1990. M. Zuker ported all the code except for the dotplt
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subroutine. Roland Gaboury created dotplt 'de novo' using the IRIS
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GL.
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METHOD : A dynamic programming algorithm is used to find optimal and
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suboptimal foldings of an RNA molecule starting from linear sequence
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data. Auxiliary information can be used to constrain the folding.
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Energy data from :
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S.M. Freier et al., Proc. Natl. Acad. Sci. USA, 83, 9373-9377, 1986.
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D.H. Turner et al., Cold Spring Harbor Symposia on Quantitative Biology,
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52, 123-133, 1987.
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D.H. Turner et al., Annu. Rev. Biophys. Biophys. Chem 17, 167-192 (1988).
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This last reference has all the dangling end and terminal mismatch data.
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References :
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M. Zuker
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On Finding All Suboptimal Foldings of an RNA Molecule.
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Science, 244, 48-52, (1989)
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J. A. Jaeger, D. H. Turner and M. Zuker
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Improved Predictions of Secondary Structures for RNA.
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Proc. Natl. Acad. Sci. USA, BIOCHEMISTRY, 86, 7706-7710, (1989)
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J. A. Jaeger, D. H. Turner and M. Zuker
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Predicting Optimal and Suboptimal Secondary Structure for RNA.
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in "Molecular Evolution: Computer Analysis of Protein and
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Nucleic Acid Sequences", R. F. Doolittle ed.
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Methods in Enzymology, 183, 281-306 (1989)
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see also:
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M. Zuker
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Computer Prediction of RNA Structure.
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in "RNA Processing", J. E. Dahlberg and J. N. Abelson eds.
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Methods in Enzymology, 180, 262-288, (1989)
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M. Zuker
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The Use of Dynamic Programming Algorithms in RNA Secondary
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Structure Prediction.
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in "Mathematical Methods for DNA Sequences", M. S. Waterman ed.
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CRC Press, Inc., 159-184, (1989)
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A.B. Jacobson, M. Zuker and A. Hirashima
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Comparitive Studies on the Secondary Structure of the RNAs of
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Related RNA Coliphages.
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in "Molecular Biology of RNA: New Perspectives", M. Inouye and
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B. S. Dudock eds.
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Academic Press, Inc., 331-354, (1987)
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Use :
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lrna and crna are ready to use. They can be run by issuing the
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commands :
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lrna
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or
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crna
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To have these programs run in their own shell, you can use the
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commands :
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zsh lrna
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or
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zsh crna
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lrna and crna have many files in common. However, the include file
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'rfd.inc' is different for lrna and crna. lrna uses lin.inc as its
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rfd.inc, and crna uses circ.inc. This is taken care of automatically
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in Makefile. The folding dimensions can be altered by changing
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lin.inc (linear RNA folding) or circ.inc (circular RNA folding). If
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lin.inc or circ.inc is changed, then ALL subroutines used by lrna or
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crna must be recompiled with the exception of formid and multid. This
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is done automatically by Makefile.
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files.list contains a list and description of all files used for
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folding. Note the sample runs of the ALU sequence and the batch input
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files (bat1.com and bat2.com that produced them).
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mfold.user is a user's manual.
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mfold.doc is a glossary of functions, subroutines and variables.
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mfold.flow is a crude flow chart of the main program of mfold.
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