Re: [Biopython] Question: Searching for RNA motifs with PSSM

Dear Peter,

Thanks for pointing this out for me! The code snippets are very
helpful!

Best,

Máté

2023. 12. 15. 13:05 keltezéssel, Peter
Cock írta:

See also this discussion for proteins:

https://github.com/biopython/biopython/issues/3636

Having the code handle RNA or DNA looks very
straightforward in comparison (e.g. treating U and u the same
as T and t in the C code).

Peter

On Fri, Dec 15, 2023 at
10:33 AM Váczy-Földi Máté <[email protected] >
wrote:

Dear Peter,

Thank thank you very much for the suggestion! I will go
ahead with this method.

Best wishes,

Máté

2023. 12. 15. 10:16 keltezéssel, Peter Cock írta:

Hello Máté,

I see you are referring to the
PositionSpecificScoringMatrix class

defined in Bio/motifs/matrix.py which does indeed
appear to be DNA

only. I can't comment on any drawbacks in
generalizing that code

(I can see how I would attempt this), but your
first idea is what I would

have suggested in the short term - map any U to T
in your motifs and

sequences to be searched (i.e. treat as DNA).

Peter

On Thu, Dec 14, 2023
at 4:18 PM Váczy-Földi Máté <[email protected] >
wrote:

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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