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README_Pfam_database.md

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How to download the full Pfam database

If you want to download the entire Pfam database (~1.6 GB, extracted)

  1. The file of our interest is Pfam-A.hmm
  2. In your download folder open a terminal and type
    • ftp ftp://ftp.ebi.ac.uk/
    • cd pub/databases/Pfam/current_release
    • get Pfam-A.hmm.gz
    • get md5_checksums
    • exit
    • md5sum --check md5_checksum
    • gzip -d Pfam-A.hmm.gz
  3. Copy your file inside the 00_hmm_profiles folder of Brivez

How to download a specific ~.hmm file

  1. Go to https://pfam.xfam.org/
  2. Click on the section "SEARCH" in the top menu
  3. Click on the section "Domain architecture" in the left menu
  4. Type the domain's name that are you looking for (i.e. PF00092 or vWA) and click Go
  5. Click on the relative accession
  6. In the left menu (inside the tab of PF00092) select "Alignments"
  7. Under the voice "Format an alignment" choice the seed or full alignment, format ~.selex and click generate
  8. Copy your file inside the 00_hmm_profiles folder of Brivez