
Hi everyone.

I am having troubles undestanding if the PFAM-A hmm's provided by the pfam database are the ones obtained by the SEED or from the FULL alignment of the family.

In the step-by-step description in pfam's website (say:   http://pfam.xfam.org/family/PF00004#tabview=tab6 ) they provide the command used to obtain the hmm form the seed, and then the command to run the 'search' performed on all  the pfamseq to obtain the "full" msa. Then they provide a "raw hmm" to download, but it is not clear to me if this hmm is the one they obtained from the seed with the given command OR another one, obtained from the full alignment; neither I unsterstand if it is supposed to be the same hmm i can find in the ftp website in the file PFAM-A.hmm

In the PFAM papers i cannot find any paragraph citing the "full-msa" hmm, but I've head about it from many people. Maybe they are wrong Or i am not good in reading pfam's papers and documentation, but it's days i am struggling with this and I still cannot find some clear definition of all the databases and the hmms used to build them.


I was once confused by this. It seems definitions are not as clear in bioinformatics as they are in mathematics and misunderstanding is common. If you click on the 'download' link once you follow your link above you will see the NSEQ field which has the value 207. This seed alignment defines the family. 

Sometimes the HMM model is called the alignment, sometimes all the sequences lined up together is called the alignment. The full alignment is what results when executing an HMM search based on the seed alignment. The full alignment does not define a family since it changes as new sequence data is ingested. 