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This is the main program of MiGaL. migal
is used to compare two RNA secondary structures. Various file formats
are supported: bpseq, ct, ct2, dot/parenthesis and MiGaL xml format.
Basically, to compare two
structures encoded in file1
and file2
use migal -M file1 file2
. The option -M
indicates at which level from 0 to 3 (as described in previous page) one wants to perform the
comparison.
Here are the main options of migal:(see also migal
-h
for a complete list of options)
--memory
: The memory consumed by migal is obtained
with a mmap of 2GB (not really used). Sometimes, this is too much
and one has to tell to migal how much memory one has on the
computer, for example --memory 256
-t
:Fusion tuning parameter. High values (about 0.1)
limit fusions, low values (less than 0.001) favour fusions.--forester
: Encode the last layer like RNAforester. Allow to break nucleotide links.--hairpin-strict
:Force hairpin loops to be
associated only with hairpin loops.--indel-once
: If an element is deleted at level 1,
the cost for its deletion at levels 2 and 3 is zero.--ps1 --ps2
: Use this option to compute a coloured
version of the postscript representation of the secondary structures.
Only some formats are supported, in particular migal knows postscripts
generated with RNAplot --post ""
--all-ps
build a colored ps file for each level--filter-ps
Filter the structure using the sequence read in the postscript file. -a
: use to output an alignment of the sequences of
the RNA
based on the secondary structure comparison.-x
: this option is experimental. It allows one to
output three xml files. Two of them correspond to the input structure
and the last one
is a secondary structure model of the two structures.-l
:set the initial values for the maximum of node
fusion and edge fusion per node.-L
:set the incremental steps for maximum node fusion
and edge fusion per node. rnaconverter
is used to convert file
formats from ct, ct2, bpseq and dot/parenthesis to MiGaL xml format (or
optionaly dot/parenthesis). This program is particulary useful if your
structures contain pseudo-knots because rnaconverter
will
ask you to break some helices to remove them and so the output
structures will be pseudo-knots free. Also, rnaconverter
can check a postscript file (it checks that the format of the
postscript is supported and the number of nucleotides in the postscript
is equal to the number of nucleotides in the secondary structure file).
rna2tex
computes a TeX file that contains
the tree representation at each level of a RNA secondary structure.
This program should be used only with small structures as latex
will make stack overflow
for too big trees (can be
partially solved by editing texmf.cnf
and running update-texmf
).
Check if a postscript file format can be handle by migal.
Extract from a structure file the part which corresponds to a sequence
Color postscripts file using a sequence alignment. Can be used to color postscript files using result from other comparison tools such RNAforester.
Get the sequence of the RNA represented in a postscript file. Can be used
in jonction to filterstructure
to extract in a structure file the part
that is represented in the postscript file.
If you have a file containing a lot of secondary structure in dot/parenthesis format (one line starting with ">", one line for the sequence, one line for the structure) this script will explode each structure into a separated file.
phylo_nj.py
is used to compare many
structures together and output distance matrices. Basically phylo_nj.py
file1 file2 file3 file4
will run migal -M
for each
couple filei filej
.
If you want to set specific parameters for migal
,
you can use the -o
option.
The option -d
creates a directory for each
computation (migal is lunched into this directory
), for
example this can be used to save the alignments resulting from each
comparison (-o"-a align" -d
).
Also, you can ask to use (option -p
) a
postscript file if they are present in the same place with suffix .ps
.
The option --rnaplot
is used to build the missing
postscript using RNAplot
.
Finally, if you have phylip
installed, the
option --phylip
will compute the tree from the matrices
file using the neighbor joining method.
Take a look at the example 2 for a complete example of use and method description.
phylo.py
is used to build a phylogenetic
tree from a set of secondary structures. This script supports most of the
phylo_nj.py
options.
Take a look at the example 3 for a complete example of use and method description.
This script is used to sum two matrices (computed with
previous script). For example: merge_matrix.py Layer0 Layer1 0.6
0.4
prints a new matrix with values equal to 0.6*value in Layer0
+ 0.4*value in Layer1.