[Biopython] Question: Searching for RNA motifs with PSSM

Dear Mailing List Members,

I would like to ask a question related to the Bio.motifs package.

I am currently working a project where I need to find RNA motifs
in RNA sequences. After consideration we have decided to search
for the motif occurrences using PSSMs, and I would like to
implement this using Biopython. I looked at the relevant codes in
the in the matrix.py file and I have seen that the PSSM calculate
method is hard coded to work only with DNA. There is also a note
saying "the sequence can only be a DNA sequence".

My question is that:

- Would it be safe to replace all Us with Ts in the
sequences/PSSMs and run the search that way? (I have seen one
example of someone doing this while searching.)

- Or would it be possible for me to modify the code to work with
RNA by replacing the Ts with Us in the code (or in a more
sophisticated way providing an option for both)?

For the latter I understand that I have to modify the _pwm.c code
too. I am not experienced in C, but what I gathered by looking at
that code, it should not be a big problem.

I am just looking for some confirmation that I am not overlooking
some computational or biology related reason why the above
mentioned solutions are not possible.

Thank you in advance for your kind help!

Best wishes,

Máté Váczy-Földi

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