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Currently we just take the UniProt boundaries, which are based on Prosite annotations (profile-based regular expression searches).
We should look into whether there is a more appropriate procedure.
…
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Hi,
EffectR is a brilliant package for identifying effectors.
I just had a question regarding the identification of proteins with custom motifs. For some reason, when I use a custom pattern, the r…
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I am new to analyzing mass spectrometry data, so for my first experiment (an IP experiment with trypsin digestion), we let our mass spec core facility (the experts) run MaxQuant on the raw data for us…
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Hi,
I would like to get phosphosite level information with the top1 method with a 0.75 cutoff, instead of the 0.9 or 0.99 used to generate the matrixes.
Has the top1 method been implemented in the …
Giu-F updated
1 month ago
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The Protein Translation exercise incorrectly uses the word "protein" in place of "amino acid" in the codon mapping table in the description, and seems to use "protein" somewhat vaguely in the test dat…
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# DeepScore: Community curated scoring, supercharged with AI
![EJ2PqRjXsAIQrb6](https://user-images.githubusercontent.com/16521288/195572456-62ab95bf-d0bc-4f70-b5e4-272cb509eff4.jpeg)
(Image taken f…
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```r
> library(ensembldb)
*** output flushed ***
> library(AnnotationHub)
*** output flushed ***
> ah edb105 ensembldb:::cleanColumns(edb105, listColumns(edb105))
[1] "seq_name" …
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Hello,
ZFIN updated their GAF file to support the "AND/OR" logic (comma/pipe) in column 8.
Since this update, our GAF validation checks have been unstable. See the last one here: http://build.berkele…
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Beginning with sequence-based searches of the literature via PaperBLAST and using the sequences acquired from PomBase, UniProtKB
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Hi @edwintse @TomkUCL @lindapatio @jemimahaque
We need more about the project on the wiki - describing the story so far.
https://github.com/StructuralGenomicsConsortium/CNP4-Nsp13-C-terminus-B/…