-
MBR attempts to map identifications from one run onto peaks in another run. This is incompatible with the multiprotease search because it does not make sense to map IDs from one protease onto another …
-
Dear Soeding lab members,
After sequence clustering, I am getting some very large clusters.
I would like to obtain MSA for each cluster within reasonable computational time so I am trying to limit t…
-
I noticed that VEP 112 predicts an opposite consequence as compared to previous versions for certain insertions (rare cases). It predicts `inframe_insertion,stop_retained_variant` in cases where `fram…
-
Hi developer,
Thanks you for your program. It is quite easy to use and generate valuable results.
I want to get help with the de novo protein structure prediction using PSIPRED. I always got th…
-
The first process of train VAE was successful.
But an error occurred when train_ligand_binging_model.
polygon train_ligand_binding_model --uniprot_id Q9Y572O --binding_db_path /home/yanbosmu/Bioin…
-
Hello,
Thank you for creating this wonderful software; I foresee great success!
I am trying to run a simple unconditional monomer from my PDB file using the README.md tutorials. So I have my envir…
-
Hi,
I installed RoseTTAFold-All-Atom exactly as instructed, and then completed missing packages,
2005 pip install hydra-core --upgrade
2007 pip install icecream
2009 pip install assertp…
-
Hi David,
I was recently using OrthoFinder to look for species-specific orthogroups in a new genome that we've assembled. However, I noticed that several of the orthogroups classified as species-sp…
-
Hello,
I have been trying to run BRAKER for a while and I am running into some problems relating to protein-based annotation. I successfully ran BRAKER with rna-seq only, but when I run protein onl…
-
Hi There,
I was wondering if it is possible to define preferred representative sequences for clusters in cd-hit when there are identical sequences in a cluster.