./bin/slider.py (sfold | mfold | gcg) (mRNA | noncod) [search-path [output-preffix]]
Parse connect (ct) files from a collection of RNA sequences for secondary structure motifs.
Results are stored in csv format and can be converted to excel format by bin/csv2xml.py.
*** Copyright
Copyright by Simon Dornseifer & Georg Sczakiel (2013)
dornseifer (at) imm (dot) uni (dash) luebeck (dot) de
*** Arguments
The first argument specifies the format of the parsed connect files
sfold for ct files generated by the Sfold online sever at http://sfold.wadsworth.org/cgi-bin/srna.pl
mfold for ct files generated by the Mfold online sever at http://mfold.rna.albany.edu/?q=mfold/RNA-Folding-Form
gcg for ct files generated by Mfold from GCG Version 11.0 by Accelrys Inc.
The second argument specifies whether the searched sequences are mRNA (that is, containing start and stop codons) or non-coding RNAs (without start and stop codons).
The third argument takes the location of the search path to the sequences and connect files.
The search path should point to a folder with subfolders, each containing the sequence of an mRNA in GenRef format (ending on .txt) and a subfolder (connect) containing the connect files for the sequence. Accession number, start and stop codon locations are read from the GenRef file. If no search path is specified,the current path is searched.
The forth argument specifies the prefix of the result files which will be generated by this programme.
*** Secondary structure motifs
By default the program parses the connect files for GC helices (≥ 8 uninterrupted GC pairs, strand distance ≥ 40 nt, ≥ 16 nt of nt in linker region involved in base pairings); AU helices (≥ 8 uninterrupted AU pairs, strand distance ≥ 40 nt, ≥ 16 nt of nt in linker region involved in base pairings) and GC stem loops (≥ 8 uninterrupted GC pairs, strand distance < 40 nt, < 16 nt of nt in linker region involved in base pairings). Other pre-defined motifs can be used be commenting/uncommenting different HELIXDEF definitions or writing your own HELIXDEF definition in the main method of ./bin/slider.py
*** Sample data set
The sample data set contains the GenRef files of 77 human RNA sequences and corresponding connect files generated by Mfold 2.3 performed with window sizes of 800 nucleotides at a step width of 20 nucleotides for each mRNA sequence.
./bin/slider.py gcg mRNA ./sequences humanRNA
*** Miscellaneous
for further tools in ./bin, please refer to the python scripts directly. A more detailed documentation will follow soon.
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