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Hi folks,
I was really spending a lot of time on following. I would like to construct CG / AT skew plots around the putative T-DNA insertion sites for a 50 in their number, set of sequences (of the same length, 500 bp, taking string sequences of 250 bp upstream and downstream the insertion sites) using sliding windows of 10 bp each.
I read that one can perform a skew plotting analysis using the biopython package SeqUtils (http://biopython.org/DIST/docs/api/B...ls-module.html) source codon, specifically I would be interested for the xGC_skew function. I am trying to execute the module which is inside the package as a script code from command line but it does not work. Whilst I have installed the 1.58 biopython library, I would be grateful if someone could explain me how to execute the module either as script or inside python itself.
Any alternative suggestions on how to perform such an analysis (perl, python, R scripts) would be more than grateful!!!!
Thanks in advance
I was really spending a lot of time on following. I would like to construct CG / AT skew plots around the putative T-DNA insertion sites for a 50 in their number, set of sequences (of the same length, 500 bp, taking string sequences of 250 bp upstream and downstream the insertion sites) using sliding windows of 10 bp each.
I read that one can perform a skew plotting analysis using the biopython package SeqUtils (http://biopython.org/DIST/docs/api/B...ls-module.html) source codon, specifically I would be interested for the xGC_skew function. I am trying to execute the module which is inside the package as a script code from command line but it does not work. Whilst I have installed the 1.58 biopython library, I would be grateful if someone could explain me how to execute the module either as script or inside python itself.
Any alternative suggestions on how to perform such an analysis (perl, python, R scripts) would be more than grateful!!!!
Thanks in advance