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Summary of email to 14 Feb 2019
Astrid:
>Did we get suggestions yet from the ‘gene regulatory region’-experts on which ontological terms and hierarchies (DAGs) we should create for the regulatory …
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using the return value from `getKmerFreq`, cluster k-mers into groups of overlapping/similar k-mers (same motif?), and find closest known weight matrix.
Useful to have an option to ignore the rever…
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### Setup
I am reporting a problem with Biopython version, Python version, and operating
system as follows:
```
(py3k) C:\Users\Splab-PC\Dropbox\python\biopython>Python
Python 3.6.3 |Anaconda…
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hi， the problems is that run the pipline with 1 sample is perfectct，but my data has 50 samples,it always occurs error ，when i run the 50 samples with the parameter "--reads 'my path/*.fastq…
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Read in `motifs.txt` file.
Color sarcin-ricin-like loop motifs green, U-turns blue, etc. (see `color_motifs.pml` for first pass).
Put those color patches behind nucleotides with `move_stuff_to-back…
rhiju updated
5 years ago
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I am trying to verify the false positive rate on tombo v1.5.
I was running tombo with the following commands
For the dRNA datasets `detect_modifications alternative_model --alternate-bases 5mC --r…
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https://www.uniprot.org/uniprot/Q13825
Methylglutaconyl-CoA hydratase, mitochondrial
UniProt description says
Was originally identified as RNA-binding protein that binds in vitro to clustered 5…
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Currently Biopython relies on [Weblogo](http://weblogo.threeplusone.com/) for plotting motif logos.
I have a implementation that can be tweaked to be more Biopython compatible [here](https://github.co…
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Hi,
Working with direct RNA data. I ran modification detection on IVT (PCR data) and sample of interest.
The per-read stats file was extracted into dataframes such that I have p-values for each ge…
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In https://github.com/geneontology/go-ontology/issues/15575 @bmeldal said:
> I also found
> GO:0031422 RecQ helicase-Topo III complex:
> We annotated it in CP for yeast.
> It's defined in GO a…