====== The Pfam database ======
The Pfam (protein family) data base is one of the main repositories for hosting information about evolutionarily conserved - and potentially functionally conserved - protein (sub)-sequences. Multiple sequence alignment of such (sub-)sequences - in common jargon they are typically referred to as Pfam domains - are used for training profile hidden Markov models (Pfam uses exclusively [[general:computerenvironment:plan7_phmm|Plan7 pHMMs]]). Search algorithms, such as hmmscan or hmmsearch can then be used to identify instances of the modelled domains. Searches against the Pfam database can be performed online via the [[http://pfam.xfam.org/|Pfam]] or the [[https://www.ebi.ac.uk/Tools/hmmer/|HMMER]] webpages. Alternatively, the [[http://hmmer.org/|HMMER]] package and the [[ftp://ftp.ebi.ac.uk/pub/databases/Pfam/releases/|Pfam database]] can be downloaded for running the search locally on your computer.

Pfam provides an quick introductory tour that can be accessed via this [[https://www.ebi.ac.uk/training/online/course/pfam-quick-tour|LINK]].