Comments (4)
ManuelTgn
commented on September 26, 2024
1
Hi Cristian,
now GRAFIMO visits the VG only one time, without restarting the scan for each motif in the MEME file.
In my test cases, I observed a significant speed-up.
Feel free to suggest further improvements to our tool!
Manuel
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lucapinello
commented on September 26, 2024
Hi Cristian,
Thanks for trying Grafimo and for the suggestion.
I have CCed Manuel, the main developer of GRAFIMO so he can consider
improving this part.
Thanks,
Luca
…On Wed, Jan 26, 2022 at 8:34 PM Groza Cristian ***@***.***> wrote:
Hi,
I am trying to use GRAFIMO to scan multiple motifs in a genome graph.
I passed in a MEME file with roughly 300 motifs defined in it.
The tools works fine, but every time it finishes with one motif in the
file and moves to the next one, it re-extracts all the regions defined in
the BED file.
I am not sure it is necessary for the tool to do that, and maybe this time
costly step could be avoided?
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ManuelTgn
commented on September 26, 2024
Hi Cristian,
Thanks for considering GRAFIMO for your research and for the suggestion.
I think that we can improve the regions extraction step and avoid to repeat that operation for each motif in your MEME file.
I just opened a new branch extract_regions in GRAFIMO's repo () where I'll put some updates to the code to speed-up this step.
Let us know if you have other requests or ideas to improve GRAFIMO.
Thanks,
Manuel
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cgroza
commented on September 26, 2024
Thank you,
Otherwise, this tool is great and very fast. I can see it easily screening hundreds of motifs.
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