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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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the GlyGen team had a meeting and decided on the next species we would like to add to GlyGen over the next few releases:
* Bovine (2.7)
* Zebrafish / Hamster (2.8)
* Rice (2.9)
The number in par…
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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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I am running PyAMPA on my isolated bacterial proteome. However, the pipeline has been running since the last 4 days.
My Workstation specs are i9-11900K @3.50Hz, 64 GB RAM. How long does it usually…
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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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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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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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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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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!