Tag: UniRef90

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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