Hi everyone!

I need your help with Pfam Scan output file. There is a lot of unclear columns and the official documentation have only information about output file formats...

Where I can find good documentation for this tool? Or someone can explain me the means of columns:

alignment start/end (I think that is place in my input sequence where alignment starts/ends)

envelope start/end (I really don't have idea)

hmm start/end (I don't know)

hmm length (sometimes is larger than hmm_end - hmm_start.......why?)

bit score (i think that if is big is better than small :P, but I can't interpret this value correctly (I don't know the scale))

significance (should I use only lines with significance==1? Why?)

Mainly: I need means of start/end points (and differences between them)