Tag: UniRef90

How to map Uniref90 genes (IDs) to Antibiotic resistant genes databases?

How to map Uniref90 genes (IDs) to Antibiotic resistant genes databases? 0 I have a gene abundance table for my metagenomics data. I want to just extract antibiotic resistant genes from the table and analyze them separately. The genes are defined based on the Uniref90 database. I am wondering how…

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Uniref90 database – HUMAnN – The bioBakery help forum

Hello.I performed metagenome analysis using humann3 with the full UniRef90 database (20.7GB). I found many UniRef100-IDs in the file analyzed with UniRef90 database. Why are UniRef100-IDs included in Uniref90 database? Do I mistake anywhere?Thank you. Do you mean 1) that you saw IDs that looked like UniRef100_XYZ or 2) that…

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Efficient way of mapping UniProt IDs to representative UniRef90 IDs?

You can do this directly on UniProt: www.uniprot.org/uploadlists/ Just paste or upload your list of UniProt IDs, and select “UniProtKB AC/ID” in the “From” field and “UniParc” in the “To” field I’ve also written a script, pasted below, that can do this with some useful options: $ uniprot_map.pl -h uniprot_map.pl…

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Custom genetic database – Deepmind/Alphafold

It is possible, but only with a code change in data/pipeline.py: If the database is a FASTA file, you could add a new Jackhmmer searcher for that database. You can take a look at the jackhmmer_uniref90_runner and basically follow the same logic for your database. If the database is a…

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Install alphafold on the local machine, get out of docker.

AlphaFold This package provides an implementation of the inference pipeline of AlphaFold v2.0. This is a completely new model that was entered in CASP14 and published in Nature. For simplicity, we refer to this model as AlphaFold throughout the rest of this document. Any publication that discloses findings arising from…

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get only one representative fasta sequence per family

Pfam – get only one representative fasta sequence per family 2 Hey can u help me with getting only one representative fasta sequence per family? Is there way to simply do that? cheers X pfam fasta protein • 186 views It’s not trivial. You could use the sequences from the…

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Download UniProt databases via HTTP/HTTPS instead of FTP? (Google Apps Scripts Question)

Download UniProt databases via HTTP/HTTPS instead of FTP? (Google Apps Scripts Question) 1 Hello, Does anyone know of a mirror to download the UniRef90 database via HTTP or HTTPS, or something supported by Google Apps Scripts? I want to download the UniRef90 database, but it is not possible via FTP…

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Any idea about extracting bacteria related proteins(or protein clusters) from uniref90 database?

Any idea about extracting bacteria related proteins(or protein clusters) from uniref90 database? 1 Hi guys, I want to do a blastp to align some microbial DNA sequences(fastq) against uniref90 protein catalog, in order to answer some questions about protein abundance in my data. The thing is that uniref90 fasta file…

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