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

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

_______________________________________________

Biopython mailing list - [email protected]

https://mailman.open-bio.org/mailman/listinfo/biopython

_______________________________________________
Biopython mailing list  -  [email protected]
https://mailman.open-bio.org/mailman/listinfo/biopython