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any thought how we can adopt outputs from PD to be used in this pipeline?
the problem with PD output is that the each phospho site location is given within the phosphopeptide and not the protein!
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We currently only integrate UniProt proteins that have a reference proteome ID. Do we also want to integrate the 195 UniProt reviewed entries that are not part of the species reference proteome [(entr…
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is there mass-spec data in cptac? otherwise https://www.ebi.ac.uk/pride/archive?keyword=cancer has a lot and probably a good thing to combine with?
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It looks like there might be an issue with the processing of the uniprot-proteome-.nt files for 2.7. I noticed the size of many of the nt files has decreased from the 2.6 release.
According to the …
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Hi MQ team!
I used MQ to handle phosphorylated proteome dataset. I'd like to know the occupancy (stoichiometry) of the modified peptides. However, I found no valid values in occupancy columns in th…
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https://github.com/snail123815/BIO_tools/blob/master/Genome_and_Proteome/compare_proteome.py
Need integrate other tools:
- [ ] PSI-BLAST
- [ ] phmmer
- [ ] jackhmmer
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Dear Sir/Madam,
Thank you for providing this perfect tool. I am using OMA to infer HOGs for >400 proteomes. After the database checking step and the All Vs All step (working perfectly) were perform…
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When running with an input fasta we would blast each fasta sequence.
In cases where the input is a pVACseq list of epitopes (+ VCF), we need to further discuss which sequence to blast. If blasting …
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Hi,
I am currently analysing a human transcriptome (both RNA-seq + miRNA-seq) dataset from myometrium samples for which paired proteomic data will be acquired v. soon. I was looking for approaches …
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Triples like this (this is for Rhea but I also want the same for Reactome reaction IDs):
```
.
```
![image](https://github.com/glygener/glygen-issues/assets/20584876/6d956be5-e1f8-44d1-b262…