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Hello, I ran into an error with analyzeIUPred2A() in part 2 analysis. Would you please help check if anything is wrong with my IUPred2A result file (attached)? Thank you!
[result_IUPred2A.txt](https:…
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When a storage location for the Pfam files is specified or implied (default [big_scape_dir]/pfam)
When a version of Pfam is specified or implied (default 31.0)
Then that version of the Pfam .hmm fil…
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ProteomeScout > ptmscout_web > ptmworker > helpers > pfam_tools.py
New API for accessing pfam
bj8th updated
5 years ago
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Hi,
I have been trying to use VIBRANT on linux. I installed it through Gitclone as I had trouble trying to install the usual way. I had the message saying vibrant was good to go but when I tried t…
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I have run the following code, I am using the Trinotate version 4.0 singularity:
`~/trinotate.v4.0.0.p1.simg $TRINOTATE_HOME/Trinotate --create \
--db myTrinotate.sqlite \
--trinotate_data_dir /h…
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Search for a GO term in the data portal should use a mapping file to check mapping files since the GO terms aren't stored directly in the data files.
The KEGG -> GO mapping file is https://www.geno…
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i) UCSC has a track of "PFAM domains"
ii) UCSC table ucscGenePfam, I assume there is also a RefSeqPfam table
(http://www.genome.ucsc.edu/cgi-bin/hgTables?db=hg19&hgta_group=genes&hgta_track=ucscGeneP…
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Mappings are available for both UniRef90 and UniRef50 gene families to the following systems:
MetaCyc Reactions
KEGG Orthogroups (KOs)
Pfam domains
Level-4 enzyme commission (EC) categories
E…
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PFASUM are matrices built from Pfam structural alignments ([reference](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-017-1703-z)).
The main website is down, but I found their im…
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When I try to set the pfam_hmm_loc using the following command:
$ DRAM-setup.py set_database_locations --pfam_hmm_loc /projects/datasets/dram/1.5.0/Pfam-A.hmm.dat.gz
I get the following TypeErro…